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diff --git a/package/doc/html/_modules/MDAnalysis/analysis/align.html b/package/doc/html/_modules/MDAnalysis/analysis/align.html
index 874c920edff..6e14078c764 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/align.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/align.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.align &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.align &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -146,15 +143,15 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>
 
 <span class="sd">   &gt;&gt;&gt; ref = Universe(PDB_small)</span>
 <span class="sd">   &gt;&gt;&gt; mobile = Universe(PSF,DCD)</span>
-<span class="sd">   &gt;&gt;&gt; rmsd(mobile.atoms.CA.coordinates(), ref.atoms.CA.coordinates())</span>
+<span class="sd">   &gt;&gt;&gt; rmsd(mobile.atoms.CA.positions, ref.atoms.CA.positions)</span>
 <span class="sd">   18.858259026820352</span>
 
 <span class="sd">Note that in this example translations have not been removed. In order</span>
 <span class="sd">to look at the pure rotation one needs to superimpose the centres of</span>
 <span class="sd">mass (or geometry) first:</span>
 
-<span class="sd">   &gt;&gt;&gt; ref0 =  ref.atoms.CA.coordinates() - ref.atoms.CA.centerOfMass()</span>
-<span class="sd">   &gt;&gt;&gt; mobile0 = mobile.atoms.CA.coordinates() - mobile.atoms.CA.centerOfMass()</span>
+<span class="sd">   &gt;&gt;&gt; ref0 =  ref.atoms.CA.positions - ref.atoms.CA.center_of_mass()</span>
+<span class="sd">   &gt;&gt;&gt; mobile0 = mobile.atoms.CA.positions - mobile.atoms.CA.center_of_mass()</span>
 <span class="sd">   &gt;&gt;&gt; rmsd(mobile0, ref0)</span>
 <span class="sd">    6.8093965864717951</span>
 
@@ -172,9 +169,9 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>
 
 <span class="sd">Putting all this together one can superimpose all of *mobile* onto *ref*::</span>
 
-<span class="sd">   &gt;&gt;&gt; mobile.atoms.translate(-mobile.atoms.CA.centerOfMass())</span>
+<span class="sd">   &gt;&gt;&gt; mobile.atoms.translate(-mobile.atoms.CA.center_of_mass())</span>
 <span class="sd">   &gt;&gt;&gt; mobile.atoms.rotate(R)</span>
-<span class="sd">   &gt;&gt;&gt; mobile.atoms.translate(ref.atoms.CA.centerOfMass())</span>
+<span class="sd">   &gt;&gt;&gt; mobile.atoms.translate(ref.atoms.CA.center_of_mass())</span>
 <span class="sd">   &gt;&gt;&gt; mobile.atoms.write(&quot;mobile_on_ref.pdb&quot;)</span>
 
 
@@ -183,9 +180,9 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>
 
 <span class="sd">To **fit a single structure** with :func:`alignto`::</span>
 
-<span class="sd">  &gt;&gt;&gt; ref = Universe(PSF, PDB_small)</span>
-<span class="sd">  &gt;&gt;&gt; mobile = Universe(PSF, DCD)     # we use the first frame</span>
-<span class="sd">  &gt;&gt;&gt; alignto(mobile, ref, select=&quot;protein and name CA&quot;, mass_weighted=True)</span>
+<span class="sd">   &gt;&gt;&gt; ref = Universe(PSF, PDB_small)</span>
+<span class="sd">   &gt;&gt;&gt; mobile = Universe(PSF, DCD)     # we use the first frame</span>
+<span class="sd">   &gt;&gt;&gt; alignto(mobile, ref, select=&quot;protein and name CA&quot;, mass_weighted=True)</span>
 
 <span class="sd">This will change *all* coordinates in *mobile* so that the protein</span>
 <span class="sd">C-alpha atoms are optimally superimposed (translation and rotation).</span>
@@ -402,12 +399,12 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>
 
     <span class="k">if</span> <span class="n">mass_weighted</span><span class="p">:</span>
         <span class="n">weights</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">masses</span> <span class="o">/</span> <span class="n">numpy</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">ref_atoms</span><span class="o">.</span><span class="n">masses</span><span class="p">)</span>
-        <span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span>
-        <span class="n">mobile_com</span> <span class="o">=</span> <span class="n">mobile_atoms</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span>
+        <span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span>
+        <span class="n">mobile_com</span> <span class="o">=</span> <span class="n">mobile_atoms</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span>
     <span class="k">else</span><span class="p">:</span>
         <span class="n">weights</span> <span class="o">=</span> <span class="bp">None</span>
-        <span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">()</span>
-        <span class="n">mobile_com</span> <span class="o">=</span> <span class="n">mobile_atoms</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">()</span>
+        <span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">()</span>
+        <span class="n">mobile_com</span> <span class="o">=</span> <span class="n">mobile_atoms</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">()</span>
 
     <span class="n">ref_coordinates</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span> <span class="o">-</span> <span class="n">ref_com</span>
     <span class="n">mobile_coordinates</span> <span class="o">=</span> <span class="n">mobile_atoms</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span> <span class="o">-</span> <span class="n">mobile_com</span>
@@ -547,7 +544,7 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>
 
     <span class="c"># reference centre of mass system</span>
     <span class="c"># (compatibility with pre 1.0 numpy: explicitly cast coords to float32)</span>
-    <span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
+    <span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
     <span class="n">ref_coordinates</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span> <span class="o">-</span> <span class="n">ref_com</span>
 
     <span class="c"># allocate the array for selection atom coords</span>
@@ -569,7 +566,7 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>
     <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">ts</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">frames</span><span class="p">):</span>
         <span class="c"># shift coordinates for rotation fitting</span>
         <span class="c"># selection is updated with the time frame</span>
-        <span class="n">x_com</span> <span class="o">=</span> <span class="n">traj_atoms</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
+        <span class="n">x_com</span> <span class="o">=</span> <span class="n">traj_atoms</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
         <span class="n">traj_coordinates</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">traj_atoms</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span> <span class="o">-</span> <span class="n">x_com</span>
 
         <span class="c"># Need to transpose coordinates such that the coordinate array is</span>
@@ -1015,7 +1012,7 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1024,12 +1021,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1039,7 +1035,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/contacts.html b/package/doc/html/_modules/MDAnalysis/analysis/contacts.html
index 7317cda47da..14ab068abac 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/contacts.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/contacts.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.contacts &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.contacts &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.contacts</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -615,7 +612,7 @@ <h1>Source code for MDAnalysis.analysis.contacts</h1><div class="highlight"><pre
         <span class="bp">self</span><span class="o">.</span><span class="n">timeseries</span> <span class="o">=</span> <span class="bp">None</span>  <span class="c"># final result</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">filenames</span> <span class="o">=</span> <span class="n">args</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">asUniverse</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">as_Universe</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">selections</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">selection_strings</span><span class="p">]</span>
 
@@ -849,7 +846,7 @@ <h1>Source code for MDAnalysis.analysis.contacts</h1><div class="highlight"><pre
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -858,12 +855,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -873,7 +869,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/density.html b/package/doc/html/_modules/MDAnalysis/analysis/density.html
index bee50dd3abf..e328072cb14 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/density.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/density.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.density &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.density &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.density</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -178,7 +175,7 @@ <h1>Source code for MDAnalysis.analysis.density</h1><div class="highlight"><pre>
 <span class="sd">        The &#39;gridData&#39; module from GridDataFormats could not be</span>
 <span class="sd">        imported. Please install it first.  You can try installing with</span>
 <span class="sd">        setuptools directly from the internet:</span>
-<span class="sd">    </span>
+
 <span class="sd">          easy_install GridDataFormats</span>
 
 <span class="sd">        Alternatively, download the package from</span>
@@ -191,6 +188,7 @@ <h1>Source code for MDAnalysis.analysis.density</h1><div class="highlight"><pre>
 
 <span class="kn">import</span> <span class="nn">MDAnalysis</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis.lib.util</span> <span class="kn">import</span> <span class="n">fixedwidth_bins</span><span class="p">,</span> <span class="n">iterable</span><span class="p">,</span> <span class="n">asiterable</span>
+<span class="kn">from</span> <span class="nn">MDAnalysis.lib</span> <span class="kn">import</span> <span class="n">NeighborSearch</span> <span class="k">as</span> <span class="n">NS</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis</span> <span class="kn">import</span> <span class="n">NoDataError</span><span class="p">,</span> <span class="n">MissingDataWarning</span>
 <span class="kn">from</span> <span class="nn">..</span> <span class="kn">import</span> <span class="n">units</span>
 
@@ -659,7 +657,6 @@ <h1>Source code for MDAnalysis.analysis.density</h1><div class="highlight"><pre>
     <span class="n">protein</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="n">sel2</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">use_kdtree</span><span class="p">:</span>
         <span class="c"># using faster hand-coded &#39;not within&#39; selection with kd-tree</span>
-        <span class="kn">import</span> <span class="nn">MDAnalysis.lib.KDTree.NeighborSearch</span> <span class="kn">as</span> <span class="nn">NS</span>
         <span class="kn">import</span> <span class="nn">MDAnalysis.core.AtomGroup</span>
 
         <span class="n">set_solvent</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">solvent</span><span class="p">)</span>  <span class="c"># need sets to do bulk = allsolvent - selection</span>
@@ -824,9 +821,9 @@ <h1>Source code for MDAnalysis.analysis.density</h1><div class="highlight"><pre>
 <span class="sd">        that can be easily matched to a broader density distribution.</span>
 
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="kn">from</span> <span class="nn">MDAnalysis</span> <span class="kn">import</span> <span class="n">asUniverse</span>
+        <span class="kn">from</span> <span class="nn">MDAnalysis</span> <span class="kn">import</span> <span class="n">as_Universe</span>
 
-        <span class="n">u</span> <span class="o">=</span> <span class="n">asUniverse</span><span class="p">(</span><span class="n">pdb</span><span class="p">)</span>
+        <span class="n">u</span> <span class="o">=</span> <span class="n">as_Universe</span><span class="p">(</span><span class="n">pdb</span><span class="p">)</span>
         <span class="n">group</span> <span class="o">=</span> <span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="n">atomselection</span><span class="p">)</span>
         <span class="n">coord</span> <span class="o">=</span> <span class="n">group</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span>
         <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">&quot;Selected </span><span class="si">%d</span><span class="s"> atoms (</span><span class="si">%s</span><span class="s">) out of </span><span class="si">%d</span><span class="s"> total.&quot;</span> <span class="o">%</span>
@@ -935,7 +932,7 @@ <h1>Source code for MDAnalysis.analysis.density</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -944,12 +941,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -959,7 +955,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/distances.html b/package/doc/html/_modules/MDAnalysis/analysis/distances.html
index 4376b07a480..e2194dbaec0 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/distances.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/distances.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.distances &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.distances &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.distances</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*-</span>
@@ -112,7 +109,6 @@ <h1>Source code for MDAnalysis.analysis.distances</h1><div class="highlight"><pr
 
 <span class="kn">from</span> <span class="nn">MDAnalysis.lib.distances</span> <span class="kn">import</span> <span class="n">distance_array</span><span class="p">,</span> <span class="n">self_distance_array</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis.lib._distances</span> <span class="kn">import</span> <span class="n">contact_matrix_no_pbc</span><span class="p">,</span> <span class="n">contact_matrix_pbc</span>
-<span class="kn">from</span> <span class="nn">MDAnalysis.lib.KDTree.NeighborSearch</span> <span class="kn">import</span> <span class="n">AtomNeighborSearch</span>
 
 <span class="kn">import</span> <span class="nn">logging</span>
 
@@ -201,7 +197,7 @@ <h1>Source code for MDAnalysis.analysis.distances</h1><div class="highlight"><pr
 
 <span class="sd">    Similar to &quot;*group* and (AROUND *A* *distance* and AROUND *B* *distance*)&quot;.</span>
 
-<span class="sd">    .. SeeAlso:: Makes use of :mod:`MDAnalysis.lib.KDTree.NeighborSearch`.</span>
+<span class="sd">    .. SeeAlso:: Makes use of :mod:`MDAnalysis.lib.NeighborSearch`.</span>
 
 <span class="sd">    .. versionadded: 0.7.5</span>
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -218,7 +214,7 @@ <h1>Source code for MDAnalysis.analysis.distances</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -227,12 +223,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -242,7 +237,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/gnm.html b/package/doc/html/_modules/MDAnalysis/analysis/gnm.html
index 10d24bd3032..a35c1615e72 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/gnm.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/gnm.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.gnm &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.gnm &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.gnm</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -286,7 +283,7 @@ <h1>Source code for MDAnalysis.analysis.gnm</h1><div class="highlight"><pre>
         <span class="c">#add the com from each bonus group to the ca_positions list</span>
         <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">Bonus_groups</span><span class="p">:</span>
             <span class="c">#bonus = self.u.select_atoms(item)</span>
-            <span class="n">positions</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">vstack</span><span class="p">((</span><span class="n">positions</span><span class="p">,</span> <span class="n">item</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()))</span>
+            <span class="n">positions</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">vstack</span><span class="p">((</span><span class="n">positions</span><span class="p">,</span> <span class="n">item</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()))</span>
             <span class="n">natoms</span> <span class="o">+=</span> <span class="mi">1</span>
 
         <span class="n">matrix</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">natoms</span><span class="p">,</span> <span class="n">natoms</span><span class="p">),</span> <span class="s">&quot;float&quot;</span><span class="p">)</span>
@@ -425,7 +422,7 @@ <h1>Source code for MDAnalysis.analysis.gnm</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -434,12 +431,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -449,7 +445,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html b/package/doc/html/_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html
index b5474360dd7..b1083551618 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.hbonds.hbond_analysis &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.hbonds.hbond_analysis &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../../index.html" />
+    <link rel="up" title="Module code" href="../../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../../index.html">
               <img class="logo" src="../../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.hbonds.hbond_analysis</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -393,10 +390,10 @@ <h1>Source code for MDAnalysis.analysis.hbonds.hbond_analysis</h1><div class="hi
 
 <span class="kn">from</span> <span class="nn">MDAnalysis</span> <span class="kn">import</span> <span class="n">MissingDataWarning</span><span class="p">,</span> <span class="n">NoDataError</span><span class="p">,</span> <span class="n">SelectionError</span><span class="p">,</span> <span class="n">SelectionWarning</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis.core.AtomGroup</span> <span class="kn">import</span> <span class="n">AtomGroup</span>
-<span class="kn">import</span> <span class="nn">MDAnalysis.lib.KDTree.NeighborSearch</span> <span class="kn">as</span> <span class="nn">NS</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis.lib.util</span> <span class="kn">import</span> <span class="n">parse_residue</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis.lib.mdamath</span> <span class="kn">import</span> <span class="n">norm</span><span class="p">,</span> <span class="n">angle</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis.lib.log</span> <span class="kn">import</span> <span class="n">ProgressMeter</span>
+<span class="kn">from</span> <span class="nn">MDAnalysis.lib.NeighborSearch</span> <span class="kn">import</span> <span class="n">AtomNeighborSearch</span>
 
 <span class="kn">import</span> <span class="nn">warnings</span>
 <span class="kn">import</span> <span class="nn">logging</span>
@@ -824,20 +821,24 @@ <h1>Source code for MDAnalysis.analysis.hbonds.hbond_analysis</h1><div class="hi
     <span class="k">def</span> <span class="nf">_update_selection_2</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_s2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">selection2</span><span class="p">)</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter_first</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">logger_debug</span><span class="p">(</span><span class="s">&quot;Size of selection 2 before filtering: {0} atoms&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="p">)))</span>
-            <span class="n">ns_selection_2</span> <span class="o">=</span> <span class="n">NS</span><span class="o">.</span><span class="n">AtomNeighborSearch</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="p">)</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_s2</span> <span class="o">=</span> <span class="n">ns_selection_2</span><span class="o">.</span><span class="n">search_list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s1</span><span class="p">,</span> <span class="mf">3.</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">distance</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">logger_debug</span><span class="p">(</span><span class="s">&quot;Size of selection 2: {0} atoms&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="p">)))</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">logger_debug</span><span class="p">(</span><span class="s">&#39;Size of selection 2 before filtering:&#39;</span>
+                              <span class="s">&#39; {} atoms&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="p">)))</span>
+            <span class="n">ns_selection_2</span> <span class="o">=</span> <span class="n">AtomNeighborSearch</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_s2</span> <span class="o">=</span> <span class="n">ns_selection_2</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s1</span><span class="p">,</span> <span class="mf">3.</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">distance</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">logger_debug</span><span class="p">(</span><span class="s">&#39;Size of selection 2: {0} atoms&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="p">)))</span>
         <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="p">:</span>
-             <span class="n">logger</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s">&quot;Selection 2 &#39;{0}&#39; did not select any atoms.&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">selection2</span><span class="p">)[:</span><span class="mi">80</span><span class="p">]))</span>
+            <span class="n">logger</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s">&#39;Selection 2 &quot;{}&quot; did not select any atoms.&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+                <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">selection2</span><span class="p">)[:</span><span class="mi">80</span><span class="p">]))</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_s2_donors</span> <span class="o">=</span> <span class="p">{}</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_s2_donors_h</span> <span class="o">=</span> <span class="p">{}</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_s2_acceptors</span> <span class="o">=</span> <span class="p">{}</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">selection1_type</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&#39;donor&#39;</span><span class="p">,</span> <span class="s">&#39;both&#39;</span><span class="p">):</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_s2_acceptors</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&#39; or &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">&#39;name </span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">acceptors</span><span class="p">]))</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_s2_acceptors</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span>
+                <span class="s">&#39; or &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">&#39;name </span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">acceptors</span><span class="p">]))</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">logger_debug</span><span class="p">(</span><span class="s">&quot;Selection 2 acceptors: </span><span class="si">%d</span><span class="s">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2_acceptors</span><span class="p">))</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">selection1_type</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&#39;acceptor&#39;</span><span class="p">,</span> <span class="s">&#39;both&#39;</span><span class="p">):</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_s2_donors</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&#39; or &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">&#39;name </span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">donors</span><span class="p">]))</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_s2_donors</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_s2</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span>
+                <span class="s">&#39; or &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">&#39;name </span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">donors</span><span class="p">]))</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_s2_donors_h</span> <span class="o">=</span> <span class="p">{}</span>
             <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">d</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2_donors</span><span class="p">):</span>
                 <span class="n">tmp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_bonded_hydrogens</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
@@ -943,11 +944,11 @@ <h1>Source code for MDAnalysis.analysis.hbonds.hbond_analysis</h1><div class="hi
 
             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">selection1_type</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&#39;donor&#39;</span><span class="p">,</span> <span class="s">&#39;both&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2_acceptors</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">logger_debug</span><span class="p">(</span><span class="s">&quot;Selection 1 Donors &lt;-&gt; Acceptors&quot;</span><span class="p">)</span>
-                <span class="n">ns_acceptors</span> <span class="o">=</span> <span class="n">NS</span><span class="o">.</span><span class="n">AtomNeighborSearch</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2_acceptors</span><span class="p">)</span>
+                <span class="n">ns_acceptors</span> <span class="o">=</span> <span class="n">AtomNeighborSearch</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s2_acceptors</span><span class="p">)</span>
                 <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">donor_h_set</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_s1_donors_h</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
                     <span class="n">d</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_s1_donors</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
                     <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">donor_h_set</span><span class="p">:</span>
-                        <span class="n">res</span> <span class="o">=</span> <span class="n">ns_acceptors</span><span class="o">.</span><span class="n">search_list</span><span class="p">(</span><span class="n">AtomGroup</span><span class="p">([</span><span class="n">h</span><span class="p">]),</span> <span class="bp">self</span><span class="o">.</span><span class="n">distance</span><span class="p">)</span>
+                        <span class="n">res</span> <span class="o">=</span> <span class="n">ns_acceptors</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">AtomGroup</span><span class="p">([</span><span class="n">h</span><span class="p">]),</span> <span class="bp">self</span><span class="o">.</span><span class="n">distance</span><span class="p">)</span>
                         <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">res</span><span class="p">:</span>
                             <span class="n">angle</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">calc_angle</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="n">h</span><span class="p">,</span> <span class="n">a</span><span class="p">)</span>
                             <span class="n">donor_atom</span> <span class="o">=</span> <span class="n">h</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">distance_type</span> <span class="o">!=</span> <span class="s">&#39;heavy&#39;</span> <span class="k">else</span> <span class="n">d</span>
@@ -962,11 +963,11 @@ <h1>Source code for MDAnalysis.analysis.hbonds.hbond_analysis</h1><div class="hi
                                 <span class="n">already_found</span><span class="p">[(</span><span class="n">h</span><span class="o">.</span><span class="n">index</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)]</span> <span class="o">=</span> <span class="bp">True</span>
             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">selection1_type</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&#39;acceptor&#39;</span><span class="p">,</span> <span class="s">&#39;both&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s1_acceptors</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">logger_debug</span><span class="p">(</span><span class="s">&quot;Selection 1 Acceptors &lt;-&gt; Donors&quot;</span><span class="p">)</span>
-                <span class="n">ns_acceptors</span> <span class="o">=</span> <span class="n">NS</span><span class="o">.</span><span class="n">AtomNeighborSearch</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s1_acceptors</span><span class="p">)</span>
+                <span class="n">ns_acceptors</span> <span class="o">=</span> <span class="n">AtomNeighborSearch</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_s1_acceptors</span><span class="p">)</span>
                 <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">donor_h_set</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_s2_donors_h</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
                     <span class="n">d</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_s2_donors</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
                     <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">donor_h_set</span><span class="p">:</span>
-                        <span class="n">res</span> <span class="o">=</span> <span class="n">ns_acceptors</span><span class="o">.</span><span class="n">search_list</span><span class="p">(</span><span class="n">AtomGroup</span><span class="p">([</span><span class="n">h</span><span class="p">]),</span> <span class="bp">self</span><span class="o">.</span><span class="n">distance</span><span class="p">)</span>
+                        <span class="n">res</span> <span class="o">=</span> <span class="n">ns_acceptors</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">AtomGroup</span><span class="p">([</span><span class="n">h</span><span class="p">]),</span> <span class="bp">self</span><span class="o">.</span><span class="n">distance</span><span class="p">)</span>
                         <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">res</span><span class="p">:</span>
                             <span class="k">if</span> <span class="n">remove_duplicates</span> <span class="ow">and</span> <span class="p">(</span>
                                     <span class="p">(</span><span class="n">h</span><span class="o">.</span><span class="n">index</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="ow">in</span> <span class="n">already_found</span>
@@ -1285,7 +1286,7 @@ <h1>Source code for MDAnalysis.analysis.hbonds.hbond_analysis</h1><div class="hi
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1294,12 +1295,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1309,7 +1309,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html b/package/doc/html/_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html
index 2ee0e50c1bb..9aad0ce57d4 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.hbonds.hbond_autocorrel &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.hbonds.hbond_autocorrel &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../../index.html" />
+    <link rel="up" title="Module code" href="../../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../../index.html">
               <img class="logo" src="../../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.hbonds.hbond_autocorrel</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -604,7 +601,7 @@ <h1>Source code for MDAnalysis.analysis.hbonds.hbond_autocorrel</h1><div class="
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -613,12 +610,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -628,7 +624,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/helanal.html b/package/doc/html/_modules/MDAnalysis/analysis/helanal.html
index f02fdeb01ae..d7726da1612 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/helanal.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/helanal.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.helanal &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.helanal &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
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       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.helanal</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -175,10 +172,9 @@ <h1>Source code for MDAnalysis.analysis.helanal</h1><div class="highlight"><pre>
 <span class="sd">   characteristics of alpha helices in globular proteins. *Biophysical Journal*</span>
 <span class="sd">   75(4):1935-1944.</span>
 
-<span class="sd">.. [Bansal2000] Bansal M, Kumar S, Velavan R. 2000. HELANAL - A program to</span>
-<span class="sd">   characterise helix geometry in proteins. *J Biomol Struct Dyn.*  17(5):811-9.</span>
-<span class="sd">   http://www.jbsdonline.com/c3003/c4003/HELANAL-A-Program-to-Characterize-Helix-Geometry-in-Proteins-p-811-820</span>
-<span class="sd">   -p10020.html</span>
+<span class="sd">.. [Bansal2000] Bansal M, Kumar S, Velavan R. 2000.</span>
+<span class="sd">   HELANAL - A program to characterise helix geometry in proteins.</span>
+<span class="sd">   *J Biomol Struct Dyn.*  17(5):811-819.</span>
 
 <span class="sd">Functions</span>
 <span class="sd">---------</span>
@@ -298,7 +294,7 @@ <h1>Source code for MDAnalysis.analysis.helanal</h1><div class="highlight"><pre>
 
 <span class="sd">    :Keywords:</span>
 <span class="sd">       *selection*</span>
-<span class="sd">          selection string that selects Calpha atoms [&quot;name CA&quot;]</span>
+<span class="sd">          selection string that selects Calpha atoms [``&quot;name CA&quot;``]</span>
 <span class="sd">       *start*</span>
 <span class="sd">          start residue</span>
 <span class="sd">       *end*</span>
@@ -310,28 +306,28 @@ <h1>Source code for MDAnalysis.analysis.helanal</h1><div class="highlight"><pre>
 <span class="sd">          stop analysis for time (ps) =&lt; *finish*; ``None`` goes to the</span>
 <span class="sd">          end of the trajectory [``None``]</span>
 <span class="sd">       *matrix_filename*</span>
-<span class="sd">          Output file- bending matrix [&quot;bending_matrix.dat&quot;]</span>
+<span class="sd">          Output file- bending matrix [``&quot;bending_matrix.dat&quot;``]</span>
 <span class="sd">       *origin_pdbfile*</span>
-<span class="sd">          Output file- origin pdb file [&quot;origin.pdb&quot;]</span>
+<span class="sd">          Output file- origin pdb file [``&quot;origin.pdb&quot;``]</span>
 <span class="sd">       *summary_filename*</span>
-<span class="sd">          Output file- all of the basic data [&quot;summary.txt&quot;]</span>
+<span class="sd">          Output file- all of the basic data [``&quot;summary.txt&quot;``]</span>
 <span class="sd">       *screw_filename*</span>
 <span class="sd">          Output file- local tilts of individual residues from 2 to n-1</span>
-<span class="sd">          [&quot;screw.xvg&quot;]</span>
+<span class="sd">          [``&quot;screw.xvg&quot;``]</span>
 <span class="sd">       *tilt_filename*</span>
 <span class="sd">          Output file- tilt of line of best fit applied to origin axes</span>
-<span class="sd">          [&quot;local_tilt.xvg&quot;]</span>
+<span class="sd">          [``&quot;local_tilt.xvg&quot;``]</span>
 <span class="sd">       *bend_filename*</span>
 <span class="sd">          Output file- local bend angles between successive local helix axes</span>
-<span class="sd">          [&quot;local_bend.xvg&quot;]</span>
+<span class="sd">          [``&quot;local_bend.xvg&quot;``]</span>
 <span class="sd">       *twist_filename*</span>
 <span class="sd">          Output file- local unit twist between successive helix turns</span>
-<span class="sd">          [&quot;unit_twist.xvg&quot;]</span>
+<span class="sd">          [``&quot;unit_twist.xvg&quot;``]</span>
 <span class="sd">       *prefix*</span>
 <span class="sd">          Prefix to add to all output file names; set to ``None`` to disable</span>
-<span class="sd">          [&quot;helanal__&quot;]</span>
+<span class="sd">          [``&quot;helanal__&quot;``]</span>
 <span class="sd">       *ref_axis*</span>
-<span class="sd">          Calculate tilt angle relative to the axis; if ``None`` then [0,0,1]</span>
+<span class="sd">          Calculate tilt angle relative to the axis; if ``None`` then ``[0,0,1]``</span>
 <span class="sd">          is chosen [``None``]</span>
 
 <span class="sd">    :Raises:</span>
@@ -845,7 +841,7 @@ <h1>Source code for MDAnalysis.analysis.helanal</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -854,12 +850,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -869,7 +864,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/hole.html b/package/doc/html/_modules/MDAnalysis/analysis/hole.html
index 3c5b0d92d0f..fbba1c63c93 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/hole.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/hole.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.hole &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.hole &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.hole</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -1110,7 +1107,7 @@ <h1>Source code for MDAnalysis.analysis.hole</h1><div class="highlight"><pre>
 <span class="sd">               Point inside the pore.</span>
 
 <span class="sd">               If set to ``True`` then *cpoint* is guessed as the</span>
-<span class="sd">               :meth:`~MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry` of</span>
+<span class="sd">               :meth:`~MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry` of</span>
 <span class="sd">               the *selection* from the first frame of the trajectory.</span>
 
 <span class="sd">               If *cpoint* is not set or set to ``None`` then HOLE guesses it</span>
@@ -1145,7 +1142,7 @@ <h1>Source code for MDAnalysis.analysis.hole</h1><div class="highlight"><pre>
 <span class="sd">        This method simply uses the center of geometry of the protein selection</span>
 <span class="sd">        as a guess. *selection* is &quot;protein&quot; by default.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&quot;selection&quot;</span><span class="p">,</span> <span class="s">&quot;protein&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">()</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&quot;selection&quot;</span><span class="p">,</span> <span class="s">&quot;protein&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">()</span>
 </div>
     <span class="k">def</span> <span class="nf">_process_orderparameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Read orderparameters from *data*</span>
@@ -1230,7 +1227,7 @@ <h1>Source code for MDAnalysis.analysis.hole</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1239,12 +1236,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1254,7 +1250,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/leaflet.html b/package/doc/html/_modules/MDAnalysis/analysis/leaflet.html
index 8e8317d2d33..cb078d381c8 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/leaflet.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/leaflet.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.leaflet &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.leaflet &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.leaflet</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -108,12 +105,12 @@ <h1>Source code for MDAnalysis.analysis.leaflet</h1><div class="highlight"><pre>
 <span class="sd">One can use this information to identify</span>
 
 <span class="sd">* the upper and lower leaflet of a *planar membrane* by comparing the</span>
-<span class="sd">  the :meth:`~MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry` of</span>
+<span class="sd">  the :meth:`~MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry` of</span>
 <span class="sd">  the leaflet groups, or</span>
 
 <span class="sd">* the outer and inner leaflet of a *vesicle* by comparing histograms</span>
 <span class="sd">  of distances from the centre of geometry (or possibly simply the</span>
-<span class="sd">  :meth:`~MDAnalysis.core.AtomGroup.AtomGroup.radiusOfGyration`).</span>
+<span class="sd">  :meth:`~MDAnalysis.core.AtomGroup.AtomGroup.radius_of_gyration`).</span>
 
 <span class="sd">See example scripts in the ``examples/`` directory on how to use</span>
 <span class="sd">:class:`LeafletFinder`. The function :func:`optimize_cutoff` implements a</span>
@@ -180,7 +177,7 @@ <h1>Source code for MDAnalysis.analysis.leaflet</h1><div class="highlight"><pre>
 <span class="sd">                 use fast :func:`~MDAnalysis.analysis.distances.distance_array`</span>
 <span class="sd">                 implementation [``None``].</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">universe</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">asUniverse</span><span class="p">(</span><span class="n">universe</span><span class="p">)</span>
+        <span class="n">universe</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">as_Universe</span><span class="p">(</span><span class="n">universe</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">universe</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">selectionstring</span> <span class="o">=</span> <span class="n">selectionstring</span>
         <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">selectionstring</span><span class="p">)</span> <span class="o">==</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">AtomGroup</span><span class="o">.</span><span class="n">AtomGroup</span><span class="p">:</span>
@@ -356,7 +353,7 @@ <h1>Source code for MDAnalysis.analysis.leaflet</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -365,12 +362,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -380,7 +376,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/nuclinfo.html b/package/doc/html/_modules/MDAnalysis/analysis/nuclinfo.html
index 64bd757db03..78f1a255f3d 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/nuclinfo.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/nuclinfo.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.nuclinfo &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.nuclinfo &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.nuclinfo</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -680,7 +677,7 @@ <h1>Source code for MDAnalysis.analysis.nuclinfo</h1><div class="highlight"><pre
     <span class="n">bf4</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot; ( segid </span><span class="si">%s</span><span class="s"> and resid </span><span class="si">%s</span><span class="s"> and nucleicbase ) &quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">seg3</span><span class="p">,</span> <span class="n">i</span><span class="p">))</span>
     <span class="n">bf2</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot; ( segid </span><span class="si">%s</span><span class="s"> and resid </span><span class="si">%s</span><span class="s"> and nucleicsugar ) &quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">seg2</span><span class="p">,</span> <span class="n">bp2</span><span class="p">))</span>
     <span class="n">bf3</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot; ( segid </span><span class="si">%s</span><span class="s"> and resid </span><span class="si">%s</span><span class="s"> and nucleicsugar ) &quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">seg3</span><span class="p">,</span> <span class="n">i</span><span class="p">))</span>
-    <span class="n">x</span> <span class="o">=</span> <span class="p">[</span><span class="n">bf1</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(),</span> <span class="n">bf2</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(),</span> <span class="n">bf3</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(),</span> <span class="n">bf4</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()]</span>
+    <span class="n">x</span> <span class="o">=</span> <span class="p">[</span><span class="n">bf1</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">(),</span> <span class="n">bf2</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">(),</span> <span class="n">bf3</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">(),</span> <span class="n">bf4</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()]</span>
     <span class="n">pseudo</span> <span class="o">=</span> <span class="n">mdamath</span><span class="o">.</span><span class="n">dihedral</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">-</span> <span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span>
     <span class="n">pseudo</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">rad2deg</span><span class="p">(</span><span class="n">pseudo</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">pseudo</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span>
@@ -693,7 +690,7 @@ <h1>Source code for MDAnalysis.analysis.nuclinfo</h1><div class="highlight"><pre
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -702,12 +699,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -717,7 +713,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/psa.html b/package/doc/html/_modules/MDAnalysis/analysis/psa.html
index 6c2dc282a4e..a231876696d 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/psa.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/psa.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.psa &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.psa &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.psa</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -1094,7 +1091,7 @@ <h1>Source code for MDAnalysis.analysis.psa</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1103,12 +1100,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1118,7 +1114,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/rms.html b/package/doc/html/_modules/MDAnalysis/analysis/rms.html
index bc02e12dd4a..b69f893814f 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/rms.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/rms.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.rms &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.rms &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.rms</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -479,7 +476,7 @@ <h1>Source code for MDAnalysis.analysis.rms</h1><div class="highlight"><pre>
             <span class="c"># Move to the ref_frame</span>
             <span class="c"># (coordinates MUST be stored in case the ref traj is advanced elsewhere or if ref == mobile universe)</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">reference</span><span class="o">.</span><span class="n">trajectory</span><span class="p">[</span><span class="n">ref_frame</span><span class="p">]</span>
-            <span class="n">ref_com</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ref_atoms</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span>
+            <span class="n">ref_com</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ref_atoms</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span>
             <span class="n">ref_coordinates</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ref_atoms</span><span class="o">.</span><span class="n">positions</span> <span class="o">-</span> <span class="n">ref_com</span>  <span class="c"># makes a copy</span>
             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">groupselections_atoms</span><span class="p">:</span>
                 <span class="n">groupselections_ref_coords_T_64</span> <span class="o">=</span> <span class="p">[</span>
@@ -513,7 +510,7 @@ <h1>Source code for MDAnalysis.analysis.rms</h1><div class="highlight"><pre>
         <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">ts</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">trajectory</span><span class="p">[</span><span class="n">start</span><span class="p">:</span><span class="n">stop</span><span class="p">:</span><span class="n">step</span><span class="p">]):</span>
             <span class="c"># shift coordinates for rotation fitting</span>
             <span class="c"># selection is updated with the time frame</span>
-            <span class="n">x_com</span> <span class="o">=</span> <span class="n">traj_atoms</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
+            <span class="n">x_com</span> <span class="o">=</span> <span class="n">traj_atoms</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
             <span class="n">traj_coordinates</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">traj_atoms</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span> <span class="o">-</span> <span class="n">x_com</span>
 
             <span class="n">rmsd</span><span class="p">[</span><span class="n">k</span><span class="p">,</span> <span class="p">:</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span><span class="p">,</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">time</span>
@@ -646,19 +643,19 @@ <h1>Source code for MDAnalysis.analysis.rms</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_rmsf</span> <span class="o">=</span> <span class="n">rmsf</span>
 </div>
     <span class="nd">@property</span>
-<div class="viewcode-block" id="RMSF.rmsf"><a class="viewcode-back" href="../../../documentation_pages/analysis/rms.html#MDAnalysis.analysis.rms.RMSF.rmsf">[docs]</a>    <span class="k">def</span> <span class="nf">rmsf</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">rmsf</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;RMSF data; only available after using :meth:`RMSF.run`</span>
 
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_rmsf</span>
-</pre></div></div></div>
+</pre></div></div>
 
           </div>
         </div>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -667,12 +664,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -682,7 +678,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/waterdynamics.html b/package/doc/html/_modules/MDAnalysis/analysis/waterdynamics.html
index ab63218f0fb..fdf69b94455 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/waterdynamics.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/waterdynamics.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.waterdynamics &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.waterdynamics &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.waterdynamics</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -1157,7 +1154,7 @@ <h1>Source code for MDAnalysis.analysis.waterdynamics</h1><div class="highlight"
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1166,12 +1163,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1181,7 +1177,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/analysis/x3dna.html b/package/doc/html/_modules/MDAnalysis/analysis/x3dna.html
index 31448522590..d490e51fc51 100644
--- a/package/doc/html/_modules/MDAnalysis/analysis/x3dna.html
+++ b/package/doc/html/_modules/MDAnalysis/analysis/x3dna.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.analysis.x3dna &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.analysis.x3dna &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.analysis.x3dna</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -817,7 +814,7 @@ <h1>Source code for MDAnalysis.analysis.x3dna</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -826,12 +823,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -841,7 +837,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/CRD.html b/package/doc/html/_modules/MDAnalysis/coordinates/CRD.html
index 2a5a1f9bb46..b96816403f0 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/CRD.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/CRD.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.CRD &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.CRD &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.CRD</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -294,7 +291,7 @@ <h1>Source code for MDAnalysis.coordinates.CRD</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -303,12 +300,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -318,7 +314,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/DCD.html b/package/doc/html/_modules/MDAnalysis/coordinates/DCD.html
index 0057a49bfbb..6343151a157 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/DCD.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/DCD.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.DCD &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.DCD &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
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@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
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-      <div class="sphinxsidebar">
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             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.DCD</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -227,7 +224,7 @@ <h1>Source code for MDAnalysis.coordinates.DCD</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">uc</span>
 
     <span class="nd">@dimensions.setter</span>
-<div class="viewcode-block" id="Timestep.dimensions"><a class="viewcode-back" href="../../../documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.Timestep.dimensions">[docs]</a>    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Set unitcell with (*A*, *B*, *C*, *alpha*, *beta*, *gamma*)</span>
 
 <span class="sd">        .. versionadded:: 0.9.0</span>
@@ -235,7 +232,7 @@ <h1>Source code for MDAnalysis.coordinates.DCD</h1><div class="highlight"><pre>
         <span class="c"># note that we can re-use self._ts_order with put!</span>
         <span class="n">np</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_unitcell</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ts_order</span><span class="p">,</span> <span class="n">box</span><span class="p">)</span>
 
-</div></div>
+</div>
 <div class="viewcode-block" id="DCDWriter"><a class="viewcode-back" href="../../../documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDWriter">[docs]</a><span class="k">class</span> <span class="nc">DCDWriter</span><span class="p">(</span><span class="n">base</span><span class="o">.</span><span class="n">Writer</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Writes to a DCD file</span>
 
@@ -374,7 +371,7 @@ <h1>Source code for MDAnalysis.coordinates.DCD</h1><div class="highlight"><pre>
             <span class="s">&#39;reverse&#39;</span><span class="p">,</span> <span class="s">&#39;charmm&#39;</span><span class="p">,</span> <span class="s">&#39;first&#39;</span><span class="p">,</span> <span class="s">&#39;with_unitcell&#39;</span><span class="p">]</span>
         <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">desc</span><span class="p">,</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s">&quot;LLiiiiidiPPiiii&quot;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dcd_C_str</span><span class="p">)))</span>
 
-<div class="viewcode-block" id="DCDWriter.write_next_timestep"><a class="viewcode-back" href="../../../documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDWriter.write_next_timestep">[docs]</a>    <span class="k">def</span> <span class="nf">write_next_timestep</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ts</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+<div class="viewcode-block" id="DCDWriter.write_next_timestep"><a class="viewcode-back" href="../../../documentation_pages/coordinates/LAMMPS.html#MDAnalysis.coordinates.DCD.DCDWriter.write_next_timestep">[docs]</a>    <span class="k">def</span> <span class="nf">write_next_timestep</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ts</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
         <span class="sd">&#39;&#39;&#39; write a new timestep to the dcd file</span>
 
 <span class="sd">        *ts* - timestep object containing coordinates to be written to dcd file</span>
@@ -400,7 +397,7 @@ <h1>Source code for MDAnalysis.coordinates.DCD</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_write_next_frame</span><span class="p">(</span><span class="n">pos</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">pos</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">pos</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">],</span> <span class="n">unitcell</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">frames_written</span> <span class="o">+=</span> <span class="mi">1</span>
 </div>
-<div class="viewcode-block" id="DCDWriter.convert_dimensions_to_unitcell"><a class="viewcode-back" href="../../../documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDWriter.convert_dimensions_to_unitcell">[docs]</a>    <span class="k">def</span> <span class="nf">convert_dimensions_to_unitcell</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ts</span><span class="p">,</span> <span class="n">_ts_order</span><span class="o">=</span><span class="n">Timestep</span><span class="o">.</span><span class="n">_ts_order</span><span class="p">):</span>
+<div class="viewcode-block" id="DCDWriter.convert_dimensions_to_unitcell"><a class="viewcode-back" href="../../../documentation_pages/coordinates/LAMMPS.html#MDAnalysis.coordinates.DCD.DCDWriter.convert_dimensions_to_unitcell">[docs]</a>    <span class="k">def</span> <span class="nf">convert_dimensions_to_unitcell</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ts</span><span class="p">,</span> <span class="n">_ts_order</span><span class="o">=</span><span class="n">Timestep</span><span class="o">.</span><span class="n">_ts_order</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Read dimensions from timestep *ts* and return appropriate native unitcell.</span>
 
 <span class="sd">        .. SeeAlso:: :attr:`Timestep.dimensions`</span>
@@ -421,7 +418,7 @@ <h1>Source code for MDAnalysis.coordinates.DCD</h1><div class="highlight"><pre>
         <span class="n">np</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="n">unitcell</span><span class="p">,</span> <span class="n">_ts_order</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">([</span><span class="n">lengths</span><span class="p">,</span> <span class="n">angles</span><span class="p">]))</span>
         <span class="k">return</span> <span class="n">unitcell</span>
 </div>
-<div class="viewcode-block" id="DCDWriter.close"><a class="viewcode-back" href="../../../documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDWriter.close">[docs]</a>    <span class="k">def</span> <span class="nf">close</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="DCDWriter.close"><a class="viewcode-back" href="../../../documentation_pages/coordinates/LAMMPS.html#MDAnalysis.coordinates.DCD.DCDWriter.close">[docs]</a>    <span class="k">def</span> <span class="nf">close</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Close trajectory and flush buffers.&quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">&#39;dcdfile&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">dcdfile</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_finish_dcd_write</span><span class="p">()</span>
@@ -501,7 +498,7 @@ <h1>Source code for MDAnalysis.coordinates.DCD</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_read_dcd_header</span><span class="p">()</span>
 
         <span class="c"># Convert delta to ps</span>
-        <span class="n">delta</span> <span class="o">=</span> <span class="n">mdaunits</span><span class="o">.</span><span class="n">convert</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">delta</span><span class="p">,</span> <span class="s">&#39;AKMA&#39;</span><span class="p">,</span> <span class="s">&#39;ps&#39;</span><span class="p">)</span>
+        <span class="n">delta</span> <span class="o">=</span> <span class="n">mdaunits</span><span class="o">.</span><span class="n">convert</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">delta</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">units</span><span class="p">[</span><span class="s">&#39;time&#39;</span><span class="p">],</span> <span class="s">&#39;ps&#39;</span><span class="p">)</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">_ts_kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s">&#39;dt&#39;</span><span class="p">:</span><span class="bp">self</span><span class="o">.</span><span class="n">skip_timestep</span> <span class="o">*</span> <span class="n">delta</span><span class="p">})</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">ts</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_Timestep</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span><span class="p">,</span> <span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">_ts_kwargs</span><span class="p">)</span>
@@ -574,7 +571,7 @@ <h1>Source code for MDAnalysis.coordinates.DCD</h1><div class="highlight"><pre>
         <span class="n">ts</span><span class="o">.</span><span class="n">frame</span> <span class="o">=</span> <span class="n">frame</span>
         <span class="k">return</span> <span class="n">ts</span>
 
-<div class="viewcode-block" id="DCDReader.timeseries"><a class="viewcode-back" href="../../../documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDReader.timeseries">[docs]</a>    <span class="k">def</span> <span class="nf">timeseries</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">asel</span><span class="p">,</span> <span class="n">start</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">stop</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="s">&#39;afc&#39;</span><span class="p">):</span>
+<div class="viewcode-block" id="DCDReader.timeseries"><a class="viewcode-back" href="../../../documentation_pages/coordinates/LAMMPS.html#MDAnalysis.coordinates.DCD.DCDReader.timeseries">[docs]</a>    <span class="k">def</span> <span class="nf">timeseries</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">asel</span><span class="p">,</span> <span class="n">start</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">stop</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="s">&#39;afc&#39;</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Return a subset of coordinate data for an AtomGroup</span>
 
 <span class="sd">        :Arguments:</span>
@@ -600,7 +597,7 @@ <h1>Source code for MDAnalysis.coordinates.DCD</h1><div class="highlight"><pre>
         <span class="c"># XXX needs to be implemented</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_read_timeseries</span><span class="p">(</span><span class="n">atom_numbers</span><span class="p">,</span> <span class="n">start</span><span class="p">,</span> <span class="n">stop</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="DCDReader.correl"><a class="viewcode-back" href="../../../documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDReader.correl">[docs]</a>    <span class="k">def</span> <span class="nf">correl</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">timeseries</span><span class="p">,</span> <span class="n">start</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">stop</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
+<div class="viewcode-block" id="DCDReader.correl"><a class="viewcode-back" href="../../../documentation_pages/coordinates/LAMMPS.html#MDAnalysis.coordinates.DCD.DCDReader.correl">[docs]</a>    <span class="k">def</span> <span class="nf">correl</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">timeseries</span><span class="p">,</span> <span class="n">start</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">stop</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Populate a TimeseriesCollection object with timeseries computed from the trajectory</span>
 
 <span class="sd">        :Arguments:</span>
@@ -625,7 +622,7 @@ <h1>Source code for MDAnalysis.coordinates.DCD</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">dcdfile</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">dcdfile</span> <span class="o">=</span> <span class="bp">None</span>
 
-<div class="viewcode-block" id="DCDReader.Writer"><a class="viewcode-back" href="../../../documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDReader.Writer">[docs]</a>    <span class="k">def</span> <span class="nf">Writer</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="DCDReader.Writer"><a class="viewcode-back" href="../../../documentation_pages/coordinates/LAMMPS.html#MDAnalysis.coordinates.DCD.DCDReader.Writer">[docs]</a>    <span class="k">def</span> <span class="nf">Writer</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Returns a DCDWriter for *filename* with the same parameters as this DCD.</span>
 
 <span class="sd">        All values can be changed through keyword arguments.</span>
@@ -692,7 +689,7 @@ <h1>Source code for MDAnalysis.coordinates.DCD</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -701,12 +698,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -716,7 +712,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/DLPoly.html b/package/doc/html/_modules/MDAnalysis/coordinates/DLPoly.html
index 40fc17592dd..3ef43dc6dcd 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/DLPoly.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/DLPoly.html
@@ -1,5 +1,3 @@
-
-
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   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.DLPoly &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.DLPoly &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.DLPoly</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -106,7 +103,7 @@ <h1>Source code for MDAnalysis.coordinates.DLPoly</h1><div class="highlight"><pr
 <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">base</span>
 <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">core</span>
 
-<span class="n">_DLPOLY_UNITS</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;length&#39;</span><span class="p">:</span> <span class="s">&#39;Angstrom&#39;</span><span class="p">,</span> <span class="s">&#39;velocity&#39;</span><span class="p">:</span> <span class="s">&#39;Angstrom/ps&#39;</span><span class="p">}</span>
+<span class="n">_DLPOLY_UNITS</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;length&#39;</span><span class="p">:</span> <span class="s">&#39;Angstrom&#39;</span><span class="p">,</span> <span class="s">&#39;velocity&#39;</span><span class="p">:</span> <span class="s">&#39;Angstrom/ps&#39;</span><span class="p">,</span> <span class="s">&#39;time&#39;</span><span class="p">:</span> <span class="s">&#39;ps&#39;</span><span class="p">}</span>
 
 
 <span class="k">class</span> <span class="nc">Timestep</span><span class="p">(</span><span class="n">base</span><span class="o">.</span><span class="n">Timestep</span><span class="p">):</span>
@@ -349,7 +346,7 @@ <h1>Source code for MDAnalysis.coordinates.DLPoly</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -358,12 +355,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -373,7 +369,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/DMS.html b/package/doc/html/_modules/MDAnalysis/coordinates/DMS.html
index 2b9e7f8e94a..3d2ea0afca1 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/DMS.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/DMS.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.DMS &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.DMS &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.DMS</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -207,7 +204,7 @@ <h1>Source code for MDAnalysis.coordinates.DMS</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -216,12 +213,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -231,7 +227,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/GRO.html b/package/doc/html/_modules/MDAnalysis/coordinates/GRO.html
index 60784048ebe..994245c1e4f 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/GRO.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/GRO.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.GRO &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.GRO &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.GRO</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -354,7 +351,7 @@ <h1>Source code for MDAnalysis.coordinates.GRO</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -363,12 +360,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -378,7 +374,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/LAMMPS.html b/package/doc/html/_modules/MDAnalysis/coordinates/LAMMPS.html
index bf4599cb14d..94a5041a52b 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/LAMMPS.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/LAMMPS.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.LAMMPS &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.LAMMPS &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.LAMMPS</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -225,7 +222,7 @@ <h1>Source code for MDAnalysis.coordinates.LAMMPS</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -234,12 +231,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -249,7 +245,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/PDB.html b/package/doc/html/_modules/MDAnalysis/coordinates/PDB.html
index 22622930c15..86563c0bd27 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/PDB.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/PDB.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.PDB &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.PDB &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.PDB</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -598,8 +595,12 @@ <h1>Source code for MDAnalysis.coordinates.PDB</h1><div class="highlight"><pre>
                         <span class="k">continue</span>
                     <span class="bp">self</span><span class="o">.</span><span class="n">ts</span><span class="o">.</span><span class="n">_pos</span><span class="p">[</span><span class="n">pos</span><span class="p">]</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="p">[</span><span class="n">line</span><span class="p">[</span><span class="mi">30</span><span class="p">:</span><span class="mi">38</span><span class="p">],</span> <span class="n">line</span><span class="p">[</span><span class="mi">38</span><span class="p">:</span><span class="mi">46</span><span class="p">],</span> <span class="n">line</span><span class="p">[</span><span class="mi">46</span><span class="p">:</span><span class="mi">54</span><span class="p">]])</span>
                     <span class="n">pos</span> <span class="o">+=</span> <span class="mi">1</span>
-                    <span class="n">occupancy</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">54</span><span class="p">:</span><span class="mi">60</span><span class="p">])</span>
-                    <span class="bp">self</span><span class="o">.</span><span class="n">_occupancy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">occupancy</span><span class="p">)</span>
+                    <span class="k">try</span><span class="p">:</span>
+                        <span class="n">occupancy</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">54</span><span class="p">:</span><span class="mi">60</span><span class="p">])</span>
+                    <span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
+                        <span class="k">pass</span>
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_occupancy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">occupancy</span><span class="p">)</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">header</span> <span class="o">=</span> <span class="n">header</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">title</span> <span class="o">=</span> <span class="n">title</span>
@@ -1389,7 +1390,7 @@ <h1>Source code for MDAnalysis.coordinates.PDB</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1398,12 +1399,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1413,7 +1413,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/PDBQT.html b/package/doc/html/_modules/MDAnalysis/coordinates/PDBQT.html
index 4a929790d70..389aaadfe1e 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/PDBQT.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/PDBQT.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.PDBQT &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.PDBQT &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.PDBQT</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -454,7 +451,7 @@ <h1>Source code for MDAnalysis.coordinates.PDBQT</h1><div class="highlight"><pre
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -463,12 +460,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -478,7 +474,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/PQR.html b/package/doc/html/_modules/MDAnalysis/coordinates/PQR.html
index 61ec8f20ad8..1ed8b39df7a 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/PQR.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/PQR.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.PQR &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.PQR &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.PQR</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -316,7 +313,7 @@ <h1>Source code for MDAnalysis.coordinates.PQR</h1><div class="highlight"><pre>
             <span class="c"># Header</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_write_REMARK</span><span class="p">(</span><span class="n">pqrfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">remarks</span><span class="p">)</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_write_REMARK</span><span class="p">(</span><span class="n">pqrfile</span><span class="p">,</span> <span class="s">&quot;Input: frame {0} of {1}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">frame</span><span class="p">,</span> <span class="n">u</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">filename</span><span class="p">),</span> <span class="mi">5</span><span class="p">)</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_write_REMARK</span><span class="p">(</span><span class="n">pqrfile</span><span class="p">,</span> <span class="s">&quot;total charge: {0:+8.4f} e&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">atoms</span><span class="o">.</span><span class="n">totalCharge</span><span class="p">()),</span> <span class="mi">6</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_write_REMARK</span><span class="p">(</span><span class="n">pqrfile</span><span class="p">,</span> <span class="s">&quot;total charge: {0:+8.4f} e&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">atoms</span><span class="o">.</span><span class="n">total_charge</span><span class="p">()),</span> <span class="mi">6</span><span class="p">)</span>
             <span class="c"># Atom descriptions and coords</span>
             <span class="k">for</span> <span class="n">atom_index</span><span class="p">,</span> <span class="n">atom</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">atoms</span><span class="p">):</span>
                 <span class="n">XYZ</span> <span class="o">=</span> <span class="n">coordinates</span><span class="p">[</span><span class="n">atom_index</span><span class="p">]</span>
@@ -354,7 +351,7 @@ <h1>Source code for MDAnalysis.coordinates.PQR</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -363,12 +360,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -378,7 +374,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/TRJ.html b/package/doc/html/_modules/MDAnalysis/coordinates/TRJ.html
index 606b20e939e..4f7c4ee72bf 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/TRJ.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/TRJ.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.TRJ &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.TRJ &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.TRJ</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -384,7 +381,7 @@ <h1>Source code for MDAnalysis.coordinates.TRJ</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">periodic</span>
 
     <span class="nd">@property</span>
-<div class="viewcode-block" id="TRJReader.n_frames"><a class="viewcode-back" href="../../../documentation_pages/coordinates/TRJ.html#MDAnalysis.coordinates.TRJ.TRJReader.n_frames">[docs]</a>    <span class="k">def</span> <span class="nf">n_frames</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">n_frames</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Number of frames (obtained from reading the whole trajectory).&quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_frames</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>  <span class="c"># return cached value</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_frames</span>
@@ -394,7 +391,7 @@ <h1>Source code for MDAnalysis.coordinates.TRJ</h1><div class="highlight"><pre>
             <span class="k">return</span> <span class="mi">0</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_frames</span>
-</div>
+
     <span class="k">def</span> <span class="nf">_read_trj_n_frames</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_reopen</span><span class="p">()</span>
 
@@ -888,7 +885,7 @@ <h1>Source code for MDAnalysis.coordinates.TRJ</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -897,12 +894,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -912,7 +908,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/TRZ.html b/package/doc/html/_modules/MDAnalysis/coordinates/TRZ.html
index e6c90d7967f..042233aa362 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/TRZ.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/TRZ.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.TRZ &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.TRZ &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.TRZ</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -154,6 +151,7 @@ <h1>Source code for MDAnalysis.coordinates.TRZ</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">import</span> <span class="nn">errno</span>
+<span class="kn">import</span> <span class="nn">weakref</span>
 
 <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">base</span>
 <span class="kn">from</span> <span class="nn">..core</span> <span class="kn">import</span> <span class="n">flags</span>
@@ -178,7 +176,7 @@ <h1>Source code for MDAnalysis.coordinates.TRZ</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">triclinic_box</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">)</span>
 
     <span class="nd">@dimensions.setter</span>
-<div class="viewcode-block" id="Timestep.dimensions"><a class="viewcode-back" href="../../../documentation_pages/coordinates/TRZ.html#MDAnalysis.coordinates.TRZ.Timestep.dimensions">[docs]</a>    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Set the Timestep dimensions with MDAnalysis format cell</span>
 <span class="sd">        (*A*, *B*, *C*, *alpha*, *beta*, *gamma*)</span>
 
@@ -186,7 +184,7 @@ <h1>Source code for MDAnalysis.coordinates.TRZ</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_unitcell</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">triclinic_vectors</span><span class="p">(</span><span class="n">box</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">9</span><span class="p">)</span>
 
-</div></div>
+</div>
 <div class="viewcode-block" id="TRZReader"><a class="viewcode-back" href="../../../documentation_pages/coordinates/TRZ.html#MDAnalysis.coordinates.TRZ.TRZReader">[docs]</a><span class="k">class</span> <span class="nc">TRZReader</span><span class="p">(</span><span class="n">base</span><span class="o">.</span><span class="n">Reader</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot; Reads an IBIsCO or YASP trajectory file</span>
 
@@ -209,6 +207,7 @@ <h1>Source code for MDAnalysis.coordinates.TRZ</h1><div class="highlight"><pre>
 <span class="sd">       Frames now 0-based instead of 1-based</span>
 <span class="sd">       Extra data (Temperature, Energies, Pressures, etc) now read</span>
 <span class="sd">       into ts.data dictionary</span>
+<span class="sd">       Now passes a weakref of self to ts (ts._reader)</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="n">format</span> <span class="o">=</span> <span class="s">&quot;TRZ&quot;</span>
@@ -238,6 +237,7 @@ <h1>Source code for MDAnalysis.coordinates.TRZ</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_read_trz_header</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">ts</span> <span class="o">=</span> <span class="n">Timestep</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span><span class="p">,</span> <span class="n">velocities</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">forces</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">has_force</span><span class="p">,</span>
                            <span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">_ts_kwargs</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ts</span><span class="o">.</span><span class="n">_reader</span> <span class="o">=</span> <span class="n">weakref</span><span class="o">.</span><span class="n">ref</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
 
         <span class="c"># structured dtype of a single trajectory frame</span>
         <span class="n">readarg</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">n_atoms</span><span class="p">)</span> <span class="o">+</span> <span class="s">&#39;f4&#39;</span>
@@ -339,19 +339,19 @@ <h1>Source code for MDAnalysis.coordinates.TRZ</h1><div class="highlight"><pre>
             <span class="k">return</span> <span class="n">ts</span>
 
     <span class="nd">@property</span>
-<div class="viewcode-block" id="TRZReader.n_atoms"><a class="viewcode-back" href="../../../documentation_pages/coordinates/TRZ.html#MDAnalysis.coordinates.TRZ.TRZReader.n_atoms">[docs]</a>    <span class="k">def</span> <span class="nf">n_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">n_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Number of atoms in a frame&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_atoms</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;n_frames&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="TRZReader.n_frames"><a class="viewcode-back" href="../../../documentation_pages/coordinates/TRZ.html#MDAnalysis.coordinates.TRZ.TRZReader.n_frames">[docs]</a>    <span class="k">def</span> <span class="nf">n_frames</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">n_frames</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Total number of frames in a trajectory&quot;&quot;&quot;</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_read_trz_n_frames</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trzfile</span><span class="p">)</span>
         <span class="k">except</span> <span class="ne">IOError</span><span class="p">:</span>
             <span class="k">return</span> <span class="mi">0</span>
-</div>
+
     <span class="k">def</span> <span class="nf">_read_trz_n_frames</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trzfile</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Uses size of file and dtype information to determine how many frames exist</span>
 
@@ -367,9 +367,7 @@ <h1>Source code for MDAnalysis.coordinates.TRZ</h1><div class="highlight"><pre>
 
         <span class="k">return</span> <span class="n">nframes</span>
 
-    <span class="nd">@property</span>
-    <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;dt&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="TRZReader.dt"><a class="viewcode-back" href="../../../documentation_pages/coordinates/TRZ.html#MDAnalysis.coordinates.TRZ.TRZReader.dt">[docs]</a>    <span class="k">def</span> <span class="nf">dt</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">_get_dt</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;The amount of time between frames in ps</span>
 
 <span class="sd">        Assumes that this step is constant (ie. 2 trajectories with different steps haven&#39;t been</span>
@@ -388,16 +386,16 @@ <h1>Source code for MDAnalysis.coordinates.TRZ</h1><div class="highlight"><pre>
             <span class="k">return</span> <span class="n">dt</span>
         <span class="k">finally</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_read_frame</span><span class="p">(</span><span class="n">curr_frame</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;delta&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="TRZReader.delta"><a class="viewcode-back" href="../../../documentation_pages/coordinates/TRZ.html#MDAnalysis.coordinates.TRZ.TRZReader.delta">[docs]</a>    <span class="k">def</span> <span class="nf">delta</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">delta</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;MD integration timestep&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">dt</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">skip_timestep</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;skip_timestep&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="TRZReader.skip_timestep"><a class="viewcode-back" href="../../../documentation_pages/coordinates/TRZ.html#MDAnalysis.coordinates.TRZ.TRZReader.skip_timestep">[docs]</a>    <span class="k">def</span> <span class="nf">skip_timestep</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">skip_timestep</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Timesteps between trajectory frames&quot;&quot;&quot;</span>
         <span class="n">curr_frame</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ts</span><span class="o">.</span><span class="n">frame</span>
         <span class="k">try</span><span class="p">:</span>
@@ -411,7 +409,7 @@ <h1>Source code for MDAnalysis.coordinates.TRZ</h1><div class="highlight"><pre>
             <span class="k">return</span> <span class="n">skip_timestep</span>
         <span class="k">finally</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_read_frame</span><span class="p">(</span><span class="n">curr_frame</span><span class="p">)</span>
-</div>
+
     <span class="k">def</span> <span class="nf">_read_frame</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">frame</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Move to *frame* and fill timestep with data.</span>
 <span class="sd">        </span>
@@ -668,7 +666,7 @@ <h1>Source code for MDAnalysis.coordinates.TRZ</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -677,12 +675,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -692,7 +689,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/XYZ.html b/package/doc/html/_modules/MDAnalysis/coordinates/XYZ.html
index 1dac693dd91..c6cbf0f7f2a 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/XYZ.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/XYZ.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.XYZ &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.XYZ &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.XYZ</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -355,10 +352,10 @@ <h1>Source code for MDAnalysis.coordinates.XYZ</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_read_next_timestep</span><span class="p">()</span>
 
     <span class="nd">@property</span>
-<div class="viewcode-block" id="XYZReader.n_atoms"><a class="viewcode-back" href="../../../documentation_pages/coordinates/XYZ.html#MDAnalysis.coordinates.XYZ.XYZReader.n_atoms">[docs]</a>    <span class="k">def</span> <span class="nf">n_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">n_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;number of atoms in a frame&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_atoms</span>
-</div>
+
     <span class="k">def</span> <span class="nf">_read_xyz_natoms</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
         <span class="c"># this assumes that this is only called once at startup and that the filestream is already open</span>
         <span class="c"># (FRAGILE)</span>
@@ -476,7 +473,7 @@ <h1>Source code for MDAnalysis.coordinates.XYZ</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -485,12 +482,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -500,7 +496,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/base.html b/package/doc/html/_modules/MDAnalysis/coordinates/base.html
index eb00c32a952..80cbcc55327 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/base.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/base.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.base &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.base &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -198,6 +195,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">bisect</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">copy</span>
+<span class="kn">import</span> <span class="nn">weakref</span>
 
 <span class="kn">from</span> <span class="nn">..core</span> <span class="kn">import</span> <span class="n">flags</span>
 <span class="kn">from</span> <span class="nn">..</span> <span class="kn">import</span> <span class="n">units</span>
@@ -206,7 +204,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">..</span> <span class="kn">import</span> <span class="n">NoDataError</span>
 
 
-<div class="viewcode-block" id="Timestep"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep">[docs]</a><span class="k">class</span> <span class="nc">Timestep</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.Timestep">[docs]</a><span class="k">class</span> <span class="nc">Timestep</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Timestep data for one frame</span>
 
 <span class="sd">    :Methods:</span>
@@ -225,7 +223,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">order</span> <span class="o">=</span> <span class="s">&#39;F&#39;</span>
 
-<div class="viewcode-block" id="Timestep.__init__"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.__init__">[docs]</a>    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">n_atoms</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep.__init__"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.Timestep.__init__">[docs]</a>    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">n_atoms</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Create a Timestep, representing a frame of a trajectory</span>
 
 <span class="sd">        :Arguments:</span>
@@ -279,7 +277,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_unitcell</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_init_unitcell</span><span class="p">()</span>
 </div>
     <span class="nd">@classmethod</span>
-<div class="viewcode-block" id="Timestep.from_timestep"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.from_timestep">[docs]</a>    <span class="k">def</span> <span class="nf">from_timestep</span><span class="p">(</span><span class="n">cls</span><span class="p">,</span> <span class="n">other</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep.from_timestep"><a class="viewcode-back" href="../../../documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.DCD.Timestep.from_timestep">[docs]</a>    <span class="k">def</span> <span class="nf">from_timestep</span><span class="p">(</span><span class="n">cls</span><span class="p">,</span> <span class="n">other</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Create a copy of another Timestep, in the format of this Timestep</span>
 
 <span class="sd">        .. versionadded:: 0.11.0</span>
@@ -301,19 +299,21 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="k">except</span> <span class="n">NoDataError</span><span class="p">:</span>
             <span class="k">pass</span>
 
-        <span class="k">for</span> <span class="n">att</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&#39;_frame&#39;</span><span class="p">,</span> <span class="s">&#39;_time&#39;</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">att</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&#39;_frame&#39;</span><span class="p">,):</span>
             <span class="k">try</span><span class="p">:</span>
                 <span class="nb">setattr</span><span class="p">(</span><span class="n">ts</span><span class="p">,</span> <span class="n">att</span><span class="p">,</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">att</span><span class="p">))</span>
             <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
                 <span class="k">pass</span>
 
-        <span class="n">ts</span><span class="o">.</span><span class="n">time</span> <span class="o">=</span> <span class="n">other</span><span class="o">.</span><span class="n">time</span>
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">ts</span><span class="p">,</span> <span class="s">&#39;_reader&#39;</span><span class="p">):</span>
+            <span class="n">other</span><span class="o">.</span><span class="n">_reader</span> <span class="o">=</span> <span class="n">weakref</span><span class="o">.</span><span class="n">ref</span><span class="p">(</span><span class="n">ts</span><span class="o">.</span><span class="n">_reader</span><span class="p">())</span>
+
         <span class="n">ts</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
 
         <span class="k">return</span> <span class="n">ts</span>
 </div>
     <span class="nd">@classmethod</span>
-<div class="viewcode-block" id="Timestep.from_coordinates"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.from_coordinates">[docs]</a>    <span class="k">def</span> <span class="nf">from_coordinates</span><span class="p">(</span><span class="n">cls</span><span class="p">,</span> <span class="n">positions</span><span class="p">,</span> <span class="n">velocities</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">forces</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep.from_coordinates"><a class="viewcode-back" href="../../../documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.DCD.Timestep.from_coordinates">[docs]</a>    <span class="k">def</span> <span class="nf">from_coordinates</span><span class="p">(</span><span class="n">cls</span><span class="p">,</span> <span class="n">positions</span><span class="p">,</span> <span class="n">velocities</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">forces</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Create an instance of this Timestep, from coordinate data</span>
 
 <span class="sd">        .. versionadded:: 0.11.0</span>
@@ -330,12 +330,12 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
 
         <span class="k">return</span> <span class="n">ts</span>
 </div>
-<div class="viewcode-block" id="Timestep._init_unitcell"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep._init_unitcell">[docs]</a>    <span class="k">def</span> <span class="nf">_init_unitcell</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep._init_unitcell"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.Timestep._init_unitcell">[docs]</a>    <span class="k">def</span> <span class="nf">_init_unitcell</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Create custom datastructure for :attr:`_unitcell`.&quot;&quot;&quot;</span>
         <span class="c"># override for other Timesteps</span>
         <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">6</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="Timestep.__eq__"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.__eq__">[docs]</a>    <span class="k">def</span> <span class="nf">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep.__eq__"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.Timestep.__eq__">[docs]</a>    <span class="k">def</span> <span class="nf">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Compare with another Timestep</span>
 
 <span class="sd">        .. versionadded:: 0.11.0</span>
@@ -365,7 +365,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
 
         <span class="k">return</span> <span class="bp">True</span>
 </div>
-<div class="viewcode-block" id="Timestep.__getitem__"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.__getitem__">[docs]</a>    <span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atoms</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep.__getitem__"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.Timestep.__getitem__">[docs]</a>    <span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atoms</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Get a selection of coordinates</span>
 
 <span class="sd">        ``ts[i]``</span>
@@ -388,7 +388,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="nf">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span>
 
-<div class="viewcode-block" id="Timestep.__iter__"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.__iter__">[docs]</a>    <span class="k">def</span> <span class="nf">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep.__iter__"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.Timestep.__iter__">[docs]</a>    <span class="k">def</span> <span class="nf">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Iterate over coordinates</span>
 
 <span class="sd">        ``for x in ts``</span>
@@ -406,14 +406,14 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
             <span class="n">tail</span> <span class="o">=</span> <span class="s">&quot; &gt;&quot;</span>
         <span class="k">return</span> <span class="n">desc</span> <span class="o">+</span> <span class="n">tail</span>
 
-<div class="viewcode-block" id="Timestep.copy"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.copy">[docs]</a>    <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep.copy"><a class="viewcode-back" href="../../../documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.DCD.Timestep.copy">[docs]</a>    <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Make an independent (&quot;deep&quot;) copy of the whole :class:`Timestep`.&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__deepcopy__</span><span class="p">()</span>
 </div>
     <span class="k">def</span> <span class="nf">__deepcopy__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">from_timestep</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
 
-<div class="viewcode-block" id="Timestep.copy_slice"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.copy_slice">[docs]</a>    <span class="k">def</span> <span class="nf">copy_slice</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sel</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep.copy_slice"><a class="viewcode-back" href="../../../documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.DCD.Timestep.copy_slice">[docs]</a>    <span class="k">def</span> <span class="nf">copy_slice</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sel</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Make a new Timestep containing a subset of the original Timestep.</span>
 
 <span class="sd">        ``ts.copy_slice(slice(start, stop, skip))``</span>
@@ -448,21 +448,23 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
             <span class="n">new_TS</span><span class="o">.</span><span class="n">forces</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">forces</span><span class="p">[</span><span class="n">sel</span><span class="p">]</span>
         <span class="n">new_TS</span><span class="o">.</span><span class="n">_unitcell</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_unitcell</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
 
-        <span class="n">new_TS</span><span class="o">.</span><span class="n">time</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">time</span>
         <span class="n">new_TS</span><span class="o">.</span><span class="n">frame</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">frame</span>
 
-        <span class="k">for</span> <span class="n">att</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&#39;_frame&#39;</span><span class="p">,</span> <span class="s">&#39;_time&#39;</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">att</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&#39;_frame&#39;</span><span class="p">,):</span>
             <span class="k">try</span><span class="p">:</span>
                 <span class="nb">setattr</span><span class="p">(</span><span class="n">new_TS</span><span class="p">,</span> <span class="n">att</span><span class="p">,</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">att</span><span class="p">))</span>
             <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
                 <span class="k">pass</span>
 
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">&#39;_reader&#39;</span><span class="p">):</span>
+            <span class="n">new_TS</span><span class="o">.</span><span class="n">_reader</span> <span class="o">=</span> <span class="n">weakref</span><span class="o">.</span><span class="n">ref</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_reader</span><span class="p">())</span>
+
         <span class="n">new_TS</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
 
         <span class="k">return</span> <span class="n">new_TS</span>
 </div>
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Timestep.n_atoms"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.n_atoms">[docs]</a>    <span class="k">def</span> <span class="nf">n_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">n_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;A read only view of the number of atoms this Timestep has</span>
 
 <span class="sd">        .. versionchanged:: 0.11.0</span>
@@ -473,7 +475,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="c"># - not sure if that is ever useful</span>
         <span class="c"># - not sure how to manage existing data upon extension</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_atoms</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">has_positions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;A boolean of whether this Timestep has position data</span>
@@ -486,7 +488,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_has_positions</span>
 
     <span class="nd">@has_positions.setter</span>
-<div class="viewcode-block" id="Timestep.has_positions"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.has_positions">[docs]</a>    <span class="k">def</span> <span class="nf">has_positions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">has_positions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
         <span class="k">if</span> <span class="n">val</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_has_positions</span><span class="p">:</span>
             <span class="c"># Setting this will always reallocate position data</span>
             <span class="c"># ie</span>
@@ -497,7 +499,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="k">elif</span> <span class="ow">not</span> <span class="n">val</span><span class="p">:</span>
             <span class="c"># Unsetting val won&#39;t delete the numpy array</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_has_positions</span> <span class="o">=</span> <span class="bp">False</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">positions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;A record of the positions of all atoms in this Timestep</span>
@@ -522,10 +524,10 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="n">NoDataError</span><span class="p">(</span><span class="s">&quot;This Timestep has no positions&quot;</span><span class="p">)</span>
 
     <span class="nd">@positions.setter</span>
-<div class="viewcode-block" id="Timestep.positions"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.positions">[docs]</a>    <span class="k">def</span> <span class="nf">positions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">positions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">has_positions</span> <span class="o">=</span> <span class="bp">True</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_pos</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">new</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">_x</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;A view onto the x dimension of position data</span>
@@ -565,14 +567,14 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_has_velocities</span>
 
     <span class="nd">@has_velocities.setter</span>
-<div class="viewcode-block" id="Timestep.has_velocities"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.has_velocities">[docs]</a>    <span class="k">def</span> <span class="nf">has_velocities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">has_velocities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
         <span class="k">if</span> <span class="n">val</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_has_velocities</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_velocities</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">,</span>
                                         <span class="n">order</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">order</span><span class="p">)</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_has_velocities</span> <span class="o">=</span> <span class="bp">True</span>
         <span class="k">elif</span> <span class="ow">not</span> <span class="n">val</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_has_velocities</span> <span class="o">=</span> <span class="bp">False</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">velocities</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;A record of the velocities of all atoms in this Timestep</span>
@@ -596,10 +598,10 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="n">NoDataError</span><span class="p">(</span><span class="s">&quot;This Timestep has no velocities&quot;</span><span class="p">)</span>
 
     <span class="nd">@velocities.setter</span>
-<div class="viewcode-block" id="Timestep.velocities"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.velocities">[docs]</a>    <span class="k">def</span> <span class="nf">velocities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">velocities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">has_velocities</span> <span class="o">=</span> <span class="bp">True</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_velocities</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">new</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">has_forces</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;A boolean of whether this Timestep has force data</span>
@@ -612,14 +614,14 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_has_forces</span>
 
     <span class="nd">@has_forces.setter</span>
-<div class="viewcode-block" id="Timestep.has_forces"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.has_forces">[docs]</a>    <span class="k">def</span> <span class="nf">has_forces</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">has_forces</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
         <span class="k">if</span> <span class="n">val</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_has_forces</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_forces</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">,</span>
                                     <span class="n">order</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">order</span><span class="p">)</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_has_forces</span> <span class="o">=</span> <span class="bp">True</span>
         <span class="k">elif</span> <span class="ow">not</span> <span class="n">val</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_has_forces</span> <span class="o">=</span> <span class="bp">False</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">forces</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;A record of the forces of all atoms in this Timestep</span>
@@ -643,10 +645,10 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="n">NoDataError</span><span class="p">(</span><span class="s">&quot;This Timestep has no forces&quot;</span><span class="p">)</span>
 
     <span class="nd">@forces.setter</span>
-<div class="viewcode-block" id="Timestep.forces"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.forces">[docs]</a>    <span class="k">def</span> <span class="nf">forces</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">forces</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">has_forces</span> <span class="o">=</span> <span class="bp">True</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_forces</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">new</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;unitcell dimensions (*A*, *B*, *C*, *alpha*, *beta*, *gamma*)</span>
@@ -664,14 +666,14 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_unitcell</span>
 
     <span class="nd">@dimensions.setter</span>
-<div class="viewcode-block" id="Timestep.dimensions"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions">[docs]</a>    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_unitcell</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">box</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Timestep.volume"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.volume">[docs]</a>    <span class="k">def</span> <span class="nf">volume</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">volume</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;volume of the unitcell&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">core</span><span class="o">.</span><span class="n">box_volume</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dimensions</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">triclinic_dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;The unitcell dimensions represented as triclinic vectors</span>
@@ -703,13 +705,13 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">core</span><span class="o">.</span><span class="n">triclinic_vectors</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dimensions</span><span class="p">)</span>
 
     <span class="nd">@triclinic_dimensions.setter</span>
-<div class="viewcode-block" id="Timestep.triclinic_dimensions"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.triclinic_dimensions">[docs]</a>    <span class="k">def</span> <span class="nf">triclinic_dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">triclinic_dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Set the unitcell for this Timestep as defined by triclinic vectors</span>
 
 <span class="sd">        .. versionadded:: 0.11.0</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">dimensions</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">triclinic_box</span><span class="p">(</span><span class="o">*</span><span class="n">new</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">dt</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;The time difference in ps between timesteps</span>
@@ -722,17 +724,23 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="k">try</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;dt&#39;</span><span class="p">]</span>
         <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
-            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s">&quot;Reader has no dt information, set to 1.0 ps&quot;</span><span class="p">)</span>
-            <span class="k">return</span> <span class="mf">1.0</span>
+            <span class="k">pass</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">dt</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;dt&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_reader</span><span class="p">()</span><span class="o">.</span><span class="n">_get_dt</span><span class="p">()</span>
+            <span class="k">return</span> <span class="n">dt</span>
+        <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
+            <span class="k">pass</span>
+        <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s">&quot;Reader has no dt information, set to 1.0 ps&quot;</span><span class="p">)</span>
+        <span class="k">return</span> <span class="mf">1.0</span>
 
     <span class="nd">@dt.setter</span>
     <span class="k">def</span> <span class="nf">dt</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;dt&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">new</span>
 
     <span class="nd">@dt.deleter</span>
-<div class="viewcode-block" id="Timestep.dt"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dt">[docs]</a>    <span class="k">def</span> <span class="nf">dt</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dt</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;dt&#39;</span><span class="p">]</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">time</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;The time in ps of this timestep</span>
@@ -758,11 +766,11 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">new</span>
 
     <span class="nd">@time.deleter</span>
-<div class="viewcode-block" id="Timestep.time"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.time">[docs]</a>    <span class="k">def</span> <span class="nf">time</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">time</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time&#39;</span><span class="p">]</span>
 
-</div></div>
-<div class="viewcode-block" id="IObase"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase">[docs]</a><span class="k">class</span> <span class="nc">IObase</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+</div>
+<div class="viewcode-block" id="IObase"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.IObase">[docs]</a><span class="k">class</span> <span class="nc">IObase</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Base class bundling common functionality for trajectory I/O.</span>
 
 <span class="sd">    .. versionchanged:: 0.8</span>
@@ -775,7 +783,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
     <span class="c">#: ... for formats that support it)</span>
     <span class="n">units</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;time&#39;</span><span class="p">:</span> <span class="bp">None</span><span class="p">,</span> <span class="s">&#39;length&#39;</span><span class="p">:</span> <span class="bp">None</span><span class="p">,</span> <span class="s">&#39;velocity&#39;</span><span class="p">:</span> <span class="bp">None</span><span class="p">}</span>
 
-<div class="viewcode-block" id="IObase.convert_pos_from_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_pos_from_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_pos_from_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
+<div class="viewcode-block" id="IObase.convert_pos_from_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.IObase.convert_pos_from_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_pos_from_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;In-place conversion of coordinate array x from native units to base units.</span>
 
 <span class="sd">        By default, the input *x* is modified in place and also returned.</span>
@@ -795,7 +803,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="n">x</span> <span class="o">*=</span> <span class="n">f</span>
         <span class="k">return</span> <span class="n">x</span>
 </div>
-<div class="viewcode-block" id="IObase.convert_velocities_from_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_velocities_from_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_velocities_from_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
+<div class="viewcode-block" id="IObase.convert_velocities_from_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.IObase.convert_velocities_from_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_velocities_from_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;In-place conversion of velocities array *v* from native units to base units.</span>
 
 <span class="sd">        By default, the input *v* is modified in place and also returned.</span>
@@ -810,7 +818,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="n">v</span> <span class="o">*=</span> <span class="n">f</span>
         <span class="k">return</span> <span class="n">v</span>
 </div>
-<div class="viewcode-block" id="IObase.convert_forces_from_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_forces_from_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_forces_from_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">force</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
+<div class="viewcode-block" id="IObase.convert_forces_from_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.IObase.convert_forces_from_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_forces_from_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">force</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;In-place conversion of forces array *force* from native units to base units.</span>
 
 <span class="sd">        By default, the input *force* is modified in place and also returned.</span>
@@ -825,7 +833,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="n">force</span> <span class="o">*=</span> <span class="n">f</span>
         <span class="k">return</span> <span class="n">force</span>
 </div>
-<div class="viewcode-block" id="IObase.convert_time_from_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_time_from_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_time_from_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">t</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
+<div class="viewcode-block" id="IObase.convert_time_from_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.IObase.convert_time_from_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_time_from_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">t</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Convert time *t* from native units to base units.</span>
 
 <span class="sd">        By default, the input *t* is modified in place and also</span>
@@ -848,7 +856,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="n">t</span> <span class="o">*=</span> <span class="n">f</span>
         <span class="k">return</span> <span class="n">t</span>
 </div>
-<div class="viewcode-block" id="IObase.convert_pos_to_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_pos_to_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_pos_to_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
+<div class="viewcode-block" id="IObase.convert_pos_to_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.IObase.convert_pos_to_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_pos_to_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Conversion of coordinate array x from base units to native units.</span>
 
 <span class="sd">        By default, the input *x* is modified in place and also returned.</span>
@@ -868,7 +876,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="n">x</span> <span class="o">*=</span> <span class="n">f</span>
         <span class="k">return</span> <span class="n">x</span>
 </div>
-<div class="viewcode-block" id="IObase.convert_velocities_to_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_velocities_to_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_velocities_to_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
+<div class="viewcode-block" id="IObase.convert_velocities_to_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.IObase.convert_velocities_to_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_velocities_to_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;In-place conversion of coordinate array *v* from base units to native units.</span>
 
 <span class="sd">        By default, the input *v* is modified in place and also returned.</span>
@@ -883,7 +891,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="n">v</span> <span class="o">*=</span> <span class="n">f</span>
         <span class="k">return</span> <span class="n">v</span>
 </div>
-<div class="viewcode-block" id="IObase.convert_forces_to_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_forces_to_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_forces_to_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">force</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
+<div class="viewcode-block" id="IObase.convert_forces_to_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.IObase.convert_forces_to_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_forces_to_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">force</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;In-place conversion of force array *force* from base units to native units.</span>
 
 <span class="sd">        By default, the input *force* is modified in place and also returned.</span>
@@ -898,7 +906,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="n">force</span> <span class="o">*=</span> <span class="n">f</span>
         <span class="k">return</span> <span class="n">force</span>
 </div>
-<div class="viewcode-block" id="IObase.convert_time_to_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_time_to_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_time_to_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">t</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
+<div class="viewcode-block" id="IObase.convert_time_to_native"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.IObase.convert_time_to_native">[docs]</a>    <span class="k">def</span> <span class="nf">convert_time_to_native</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">t</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Convert time *t* from base units to native units.</span>
 
 <span class="sd">        By default, the input *t* is modified in place and also</span>
@@ -921,7 +929,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="n">t</span> <span class="o">*=</span> <span class="n">f</span>
         <span class="k">return</span> <span class="n">t</span>
 </div>
-<div class="viewcode-block" id="IObase.close"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.close">[docs]</a>    <span class="k">def</span> <span class="nf">close</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="IObase.close"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.IObase.close">[docs]</a>    <span class="k">def</span> <span class="nf">close</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Close the trajectory file.&quot;&quot;&quot;</span>
         <span class="k">pass</span>
 
@@ -1138,7 +1146,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_frames</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span><span class="p">)</span>
 
 
-<div class="viewcode-block" id="Reader"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Reader">[docs]</a><span class="k">class</span> <span class="nc">Reader</span><span class="p">(</span><span class="n">ProtoReader</span><span class="p">):</span>
+<div class="viewcode-block" id="Reader"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.Reader">[docs]</a><span class="k">class</span> <span class="nc">Reader</span><span class="p">(</span><span class="n">ProtoReader</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Base class for trajectory readers that extends :class:`ProtoReader` with a :meth:`__del__` method.</span>
 
 <span class="sd">    New Readers should subclass :class:`Reader` and properly implement a</span>
@@ -1182,7 +1190,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
 
 </div>
-<div class="viewcode-block" id="ChainReader"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ChainReader">[docs]</a><span class="k">class</span> <span class="nc">ChainReader</span><span class="p">(</span><span class="n">ProtoReader</span><span class="p">):</span>
+<div class="viewcode-block" id="ChainReader"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.ChainReader">[docs]</a><span class="k">class</span> <span class="nc">ChainReader</span><span class="p">(</span><span class="n">ProtoReader</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Reader that concatenates multiple trajectories on the fly.</span>
 
 <span class="sd">    **Known issues**</span>
@@ -1344,19 +1352,19 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
             <span class="k">return</span> <span class="bp">None</span>
 
     <span class="nd">@property</span>
-<div class="viewcode-block" id="ChainReader.frame"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ChainReader.frame">[docs]</a>    <span class="k">def</span> <span class="nf">frame</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">frame</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Cumulative frame number of the current time step.&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">ts</span><span class="o">.</span><span class="n">frame</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="ChainReader.time"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ChainReader.time">[docs]</a>    <span class="k">def</span> <span class="nf">time</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">time</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Cumulative time of the current frame in MDAnalysis time units (typically ps).&quot;&quot;&quot;</span>
         <span class="c"># currently a hack, should really use a list of trajectory lengths and delta * local_frame</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">frame</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">_default_delta</span>
         <span class="k">except</span> <span class="ne">TypeError</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">&quot;No timestep information available. Set delta to fake a constant time step.&quot;</span><span class="p">)</span>
-</div>
+
     <span class="k">def</span> <span class="nf">_apply</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Execute *method* with *kwargs* for all readers.&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="p">[</span><span class="n">reader</span><span class="o">.</span><span class="n">__getattribute__</span><span class="p">(</span><span class="n">method</span><span class="p">)(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="k">for</span> <span class="n">reader</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">readers</span><span class="p">]</span>
@@ -1388,10 +1396,10 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">__active_reader_index</span> <span class="o">=</span> <span class="n">i</span>
 
     <span class="nd">@property</span>
-<div class="viewcode-block" id="ChainReader.active_reader"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ChainReader.active_reader">[docs]</a>    <span class="k">def</span> <span class="nf">active_reader</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">active_reader</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Reader instance from which frames are being read.&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">readers</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">__active_reader_index</span><span class="p">]</span>
-</div>
+
     <span class="k">def</span> <span class="nf">_read_frame</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">frame</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Position trajectory at frame index *frame* and return :class:`Timestep`.</span>
 
@@ -1431,7 +1439,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">ts</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">__chained_trajectories_iter</span><span class="o">.</span><span class="n">next</span><span class="p">()</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">ts</span>
 
-<div class="viewcode-block" id="ChainReader.rewind"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ChainReader.rewind">[docs]</a>    <span class="k">def</span> <span class="nf">rewind</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="ChainReader.rewind"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.ChainReader.rewind">[docs]</a>    <span class="k">def</span> <span class="nf">rewind</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Set current frame to the beginning.&quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_rewind</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">__chained_trajectories_iter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_chained_iterator</span><span class="p">()</span>
@@ -1462,14 +1470,14 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
                <span class="bp">self</span><span class="o">.</span><span class="n">n_frames</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span><span class="p">)</span>
 
 </div>
-<div class="viewcode-block" id="Writer"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Writer">[docs]</a><span class="k">class</span> <span class="nc">Writer</span><span class="p">(</span><span class="n">IObase</span><span class="p">):</span>
+<div class="viewcode-block" id="Writer"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.Writer">[docs]</a><span class="k">class</span> <span class="nc">Writer</span><span class="p">(</span><span class="n">IObase</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Base class for trajectory writers.</span>
 
 <span class="sd">    See Trajectory API definition in :mod:`MDAnalysis.coordinates.__init__` for</span>
 <span class="sd">    the required attributes and methods.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-<div class="viewcode-block" id="Writer.convert_dimensions_to_unitcell"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Writer.convert_dimensions_to_unitcell">[docs]</a>    <span class="k">def</span> <span class="nf">convert_dimensions_to_unitcell</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ts</span><span class="p">):</span>
+<div class="viewcode-block" id="Writer.convert_dimensions_to_unitcell"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.Writer.convert_dimensions_to_unitcell">[docs]</a>    <span class="k">def</span> <span class="nf">convert_dimensions_to_unitcell</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ts</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Read dimensions from timestep *ts* and return appropriate unitcell.</span>
 
 <span class="sd">        The default is to return ``[A,B,C,alpha,beta,gamma]``; if this</span>
@@ -1481,7 +1489,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">convert_pos_to_native</span><span class="p">(</span><span class="n">lengths</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">([</span><span class="n">lengths</span><span class="p">,</span> <span class="n">angles</span><span class="p">])</span>
 </div>
-<div class="viewcode-block" id="Writer.write"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Writer.write">[docs]</a>    <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obj</span><span class="p">):</span>
+<div class="viewcode-block" id="Writer.write"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.Writer.write">[docs]</a>    <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obj</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Write current timestep, using the supplied *obj*.</span>
 
 <span class="sd">        The argument should be a :class:`~MDAnalysis.core.AtomGroup.AtomGroup` or</span>
@@ -1515,7 +1523,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
             <span class="c"># no trajectory loaded yet or a Writer that does not need e.g. self.n_atoms</span>
             <span class="k">return</span> <span class="s">&quot;&lt; </span><span class="si">%s</span><span class="s"> </span><span class="si">%r</span><span class="s"> &gt;&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">)</span>
 
-<div class="viewcode-block" id="Writer.has_valid_coordinates"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Writer.has_valid_coordinates">[docs]</a>    <span class="k">def</span> <span class="nf">has_valid_coordinates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">criteria</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span>
+<div class="viewcode-block" id="Writer.has_valid_coordinates"><a class="viewcode-back" href="../../../documentation_pages/coordinates/base.html#MDAnalysis.coordinates.DCD.Writer.has_valid_coordinates">[docs]</a>    <span class="k">def</span> <span class="nf">has_valid_coordinates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">criteria</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Returns ``True`` if all values are within limit values of their formats.</span>
 
 <span class="sd">        Due to rounding, the test is asymmetric (and *min* is supposed to be negative):</span>
@@ -1603,7 +1611,7 @@ <h1>Source code for MDAnalysis.coordinates.base</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1612,12 +1620,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1627,7 +1634,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/core.html b/package/doc/html/_modules/MDAnalysis/coordinates/core.html
index 9f429dc6b6a..ca4ef47c7dd 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/core.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/core.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.core &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.core &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.core</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -105,7 +102,6 @@ <h1>Source code for MDAnalysis.coordinates.core</h1><div class="highlight"><pre>
 
 <span class="sd">.. autofunction:: get_reader_for</span>
 <span class="sd">.. autofunction:: get_writer_for</span>
-<span class="sd">.. autofunction:: guess_format</span>
 
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">import</span> <span class="nn">os.path</span>
@@ -113,8 +109,7 @@ <h1>Source code for MDAnalysis.coordinates.core</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">sin</span><span class="p">,</span> <span class="n">cos</span><span class="p">,</span> <span class="n">sqrt</span>
 <span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">rad2deg</span><span class="p">,</span> <span class="n">deg2rad</span>
 
-<span class="kn">import</span> <span class="nn">MDAnalysis.coordinates</span>
-<span class="kn">import</span> <span class="nn">MDAnalysis.lib.util</span>
+<span class="kn">from</span> <span class="nn">..lib</span> <span class="kn">import</span> <span class="n">util</span>
 <span class="kn">from</span> <span class="nn">..lib.mdamath</span> <span class="kn">import</span> <span class="n">triclinic_box</span><span class="p">,</span> <span class="n">triclinic_vectors</span><span class="p">,</span> <span class="n">box_volume</span>
 
 
@@ -124,10 +119,25 @@ <h1>Source code for MDAnalysis.coordinates.core</h1><div class="highlight"><pre>
 <span class="sd">    Automatic detection is disabled when an explicit *format* is</span>
 <span class="sd">    provided.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">format</span> <span class="o">=</span> <span class="n">guess_format</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="n">format</span><span class="p">)</span>
+    <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">_trajectory_readers</span>
+
+    <span class="k">if</span> <span class="n">format</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+        <span class="n">format</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">guess_format</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+    <span class="n">format</span> <span class="o">=</span> <span class="n">format</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
     <span class="k">if</span> <span class="n">permissive</span> <span class="ow">and</span> <span class="n">format</span> <span class="o">==</span> <span class="s">&#39;PDB&#39;</span><span class="p">:</span>
-        <span class="k">return</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">_trajectory_readers</span><span class="p">[</span><span class="s">&#39;Permissive_PDB&#39;</span><span class="p">]</span>
-    <span class="k">return</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">_trajectory_readers</span><span class="p">[</span><span class="n">format</span><span class="p">]</span>
+        <span class="k">return</span> <span class="n">_trajectory_readers</span><span class="p">[</span><span class="s">&#39;Permissive_PDB&#39;</span><span class="p">]</span>
+    <span class="k">try</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">_trajectory_readers</span><span class="p">[</span><span class="n">format</span><span class="p">]</span>
+    <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+            <span class="s">&quot;Unknown coordinate trajectory format &#39;{0}&#39; for &#39;{1}&#39;. The FORMATs </span><span class="se">\n</span><span class="s">&quot;</span>
+            <span class="s">&quot;           {2}</span><span class="se">\n</span><span class="s">&quot;</span>
+            <span class="s">&quot;           are implemented in MDAnalysis.</span><span class="se">\n</span><span class="s">&quot;</span>
+            <span class="s">&quot;           See http://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1</span><span class="se">\n</span><span class="s">&quot;</span>
+            <span class="s">&quot;           Use the format keyword to explicitly set the format: &#39;Universe(...,format=FORMAT)&#39;</span><span class="se">\n</span><span class="s">&quot;</span>
+            <span class="s">&quot;           For missing formats, raise an issue at &quot;</span>
+            <span class="s">&quot;http://issues.mdanalysis.org&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+                <span class="n">format</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">_trajectory_readers</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
 
 </div>
 <div class="viewcode-block" id="reader"><a class="viewcode-back" href="../../../documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.reader">[docs]</a><span class="k">def</span> <span class="nf">reader</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
@@ -191,25 +201,27 @@ <h1>Source code for MDAnalysis.coordinates.core</h1><div class="highlight"><pre>
 <span class="sd">       Added *multiframe* keyword; the default ``None`` reflects the previous</span>
 <span class="sd">       behaviour.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
+    <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">_trajectory_writers</span><span class="p">,</span> <span class="n">_frame_writers</span>
+
     <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">)</span> <span class="ow">and</span> <span class="n">filename</span><span class="p">:</span>
-        <span class="n">root</span><span class="p">,</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">get_ext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-        <span class="n">format</span> <span class="o">=</span> <span class="n">check_compressed_format</span><span class="p">(</span><span class="n">root</span><span class="p">,</span> <span class="n">ext</span><span class="p">)</span>
+        <span class="n">root</span><span class="p">,</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">get_ext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+        <span class="n">format</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">check_compressed_format</span><span class="p">(</span><span class="n">root</span><span class="p">,</span> <span class="n">ext</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">multiframe</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
         <span class="k">try</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">_trajectory_writers</span><span class="p">[</span><span class="n">format</span><span class="p">]</span>
+            <span class="k">return</span> <span class="n">_trajectory_writers</span><span class="p">[</span><span class="n">format</span><span class="p">]</span>
         <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
             <span class="k">try</span><span class="p">:</span>
-                <span class="k">return</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">_frame_writers</span><span class="p">[</span><span class="n">format</span><span class="p">]</span>
+                <span class="k">return</span> <span class="n">_frame_writers</span><span class="p">[</span><span class="n">format</span><span class="p">]</span>
             <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
                 <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">&quot;No trajectory or frame writer for format </span><span class="si">%r</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">format</span><span class="p">)</span>
     <span class="k">elif</span> <span class="n">multiframe</span> <span class="ow">is</span> <span class="bp">True</span><span class="p">:</span>
         <span class="k">try</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">_trajectory_writers</span><span class="p">[</span><span class="n">format</span><span class="p">]</span>
+            <span class="k">return</span> <span class="n">_trajectory_writers</span><span class="p">[</span><span class="n">format</span><span class="p">]</span>
         <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">&quot;No trajectory  writer for format </span><span class="si">%r</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">format</span><span class="p">)</span>
     <span class="k">elif</span> <span class="n">multiframe</span> <span class="ow">is</span> <span class="bp">False</span><span class="p">:</span>
         <span class="k">try</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">_frame_writers</span><span class="p">[</span><span class="n">format</span><span class="p">]</span>
+            <span class="k">return</span> <span class="n">_frame_writers</span><span class="p">[</span><span class="n">format</span><span class="p">]</span>
         <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">&quot;No single frame writer for format </span><span class="si">%r</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">format</span><span class="p">)</span>
     <span class="k">else</span><span class="p">:</span>
@@ -254,103 +266,14 @@ <h1>Source code for MDAnalysis.coordinates.core</h1><div class="highlight"><pre>
     <span class="n">Writer</span> <span class="o">=</span> <span class="n">get_writer_for</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;format&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">),</span>
                             <span class="n">multiframe</span><span class="o">=</span><span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;multiframe&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">))</span>
     <span class="k">return</span> <span class="n">Writer</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">n_atoms</span><span class="o">=</span><span class="n">n_atoms</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-
-</div>
-<span class="k">def</span> <span class="nf">get_ext</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Return the lower-cased extension of *filename* without a leading dot.</span>
-
-<span class="sd">    :Returns: root, ext</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">root</span><span class="p">,</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-    <span class="k">if</span> <span class="n">ext</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">extsep</span><span class="p">):</span>
-        <span class="n">ext</span> <span class="o">=</span> <span class="n">ext</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
-    <span class="k">return</span> <span class="n">root</span><span class="p">,</span> <span class="n">ext</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
-
-
-<span class="k">def</span> <span class="nf">format_from_filename_extension</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Guess file format from the file extension&quot;&quot;&quot;</span>
-    <span class="k">try</span><span class="p">:</span>
-        <span class="n">root</span><span class="p">,</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">get_ext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-    <span class="k">except</span><span class="p">:</span>
-        <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span>
-            <span class="s">&quot;Cannot determine coordinate file format for file &#39;{0}&#39;.</span><span class="se">\n</span><span class="s">&quot;</span>
-            <span class="s">&quot;           You can set the format explicitly with &quot;</span>
-            <span class="s">&quot;&#39;Universe(..., format=FORMAT)&#39;.&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
-            <span class="c">#TypeError: ....&quot;</span>
-    <span class="n">format</span> <span class="o">=</span> <span class="n">ext</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
-    <span class="n">format</span> <span class="o">=</span> <span class="n">check_compressed_format</span><span class="p">(</span><span class="n">root</span><span class="p">,</span> <span class="n">ext</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">format</span>
-
-
-<div class="viewcode-block" id="guess_format"><a class="viewcode-back" href="../../../documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.guess_format">[docs]</a><span class="k">def</span> <span class="nf">guess_format</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Returns the type of file *filename*.</span>
-
-<span class="sd">    The current heuristic simply looks at the filename extension but more</span>
-<span class="sd">    complicated probes could be implemented here or in the individual packages</span>
-<span class="sd">    (e.g. as static methods). *filename* can also be a stream, in which case</span>
-<span class="sd">    *filename.name* is looked at for a hint to the format if *format* is not</span>
-<span class="sd">    provided.</span>
-
-<span class="sd">    If *format* is supplied then it overrides the auto detection.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">if</span> <span class="n">format</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="k">if</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">lib</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">isstream</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
-            <span class="c"># perhaps StringIO or open stream</span>
-            <span class="k">try</span><span class="p">:</span>
-                <span class="n">format</span> <span class="o">=</span> <span class="n">format_from_filename_extension</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
-            <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
-                <span class="c"># format is None so we need to complain:</span>
-                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">&quot;guess_format requires an explicit format specifier &quot;</span>
-                                 <span class="s">&quot;for stream {0}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="c"># iterator, list, filename: simple extension checking... something more</span>
-            <span class="c"># complicated is left for the ambitious.</span>
-            <span class="c"># Note: at the moment the upper-case extension *is* the format specifier</span>
-            <span class="c"># and list of filenames is handled by ChainReader</span>
-            <span class="n">format</span> <span class="o">=</span> <span class="n">format_from_filename_extension</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">lib</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">iterable</span><span class="p">(</span>
-                <span class="n">filename</span><span class="p">)</span> <span class="k">else</span> <span class="s">&#39;CHAIN&#39;</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="c"># format was set; but a list of filenames is always handled by ChainReader</span>
-        <span class="n">format</span> <span class="o">=</span> <span class="n">format</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">lib</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">iterable</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span> <span class="k">else</span> <span class="s">&#39;CHAIN&#39;</span>
-
-    <span class="n">format</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">format</span><span class="p">)</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
-
-    <span class="c"># sanity check</span>
-    <span class="k">if</span> <span class="n">format</span> <span class="o">!=</span> <span class="s">&#39;CHAIN&#39;</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">format</span> <span class="ow">in</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">_trajectory_readers</span><span class="p">:</span>
-        <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span>
-            <span class="s">&quot;Unknown coordinate trajectory format &#39;{0}&#39; for &#39;{1}&#39;. The FORMATs </span><span class="se">\n</span><span class="s">&quot;</span>
-            <span class="s">&quot;           {2}</span><span class="se">\n</span><span class="s">&quot;</span>
-            <span class="s">&quot;           are implemented in MDAnalysis.</span><span class="se">\n</span><span class="s">&quot;</span>
-            <span class="s">&quot;           See http://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1</span><span class="se">\n</span><span class="s">&quot;</span>
-            <span class="s">&quot;           Use the format keyword to explicitly set the format: &#39;Universe(...,format=FORMAT)&#39;</span><span class="se">\n</span><span class="s">&quot;</span>
-            <span class="s">&quot;           For missing formats, raise an issue at &quot;</span>
-            <span class="s">&quot;http://issues.mdanalysis.org&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
-                <span class="n">format</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">_trajectory_readers</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
-            <span class="c">#TypeError: ....&quot;</span>
-    <span class="k">return</span> <span class="n">format</span>
-
-</div>
-<span class="k">def</span> <span class="nf">check_compressed_format</span><span class="p">(</span><span class="n">root</span><span class="p">,</span> <span class="n">ext</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Check if this is a supported gzipped/bzip2ed file format and return UPPERCASE format.&quot;&quot;&quot;</span>
-    <span class="n">filename</span> <span class="o">=</span> <span class="n">root</span> <span class="o">+</span> <span class="s">&#39;.&#39;</span> <span class="o">+</span> <span class="n">ext</span>  <span class="c"># only needed for diagnostics</span>
-    <span class="c"># XYZReader&amp;others are setup to handle both plain and compressed (bzip2, gz) files</span>
-    <span class="c"># ..so if the first file extension is bzip2 or gz, look at the one to the left of it</span>
-    <span class="k">if</span> <span class="n">ext</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&quot;bz2&quot;</span><span class="p">,</span> <span class="s">&quot;gz&quot;</span><span class="p">):</span>
-        <span class="k">try</span><span class="p">:</span>
-            <span class="n">root</span><span class="p">,</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">get_ext</span><span class="p">(</span><span class="n">root</span><span class="p">)</span>
-        <span class="k">except</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">&quot;Cannot determine coordinate format for &#39;{0}&#39;&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="n">ext</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> <span class="ow">in</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">_compressed_formats</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">&quot;Cannot handle coordinates &#39;{0}&#39; in compressed format&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
-    <span class="k">return</span> <span class="n">ext</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
-</pre></div>
+</pre></div></div>
 
           </div>
         </div>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -359,12 +282,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -374,7 +296,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/pdb/extensions.html b/package/doc/html/_modules/MDAnalysis/coordinates/pdb/extensions.html
index a71b0f37d17..6cbb256b68b 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/pdb/extensions.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/pdb/extensions.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.pdb.extensions &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.pdb.extensions &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../../index.html" />
+    <link rel="up" title="Module code" href="../../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../../index.html">
               <img class="logo" src="../../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.pdb.extensions</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -267,7 +264,7 @@ <h1>Source code for MDAnalysis.coordinates.pdb.extensions</h1><div class="highli
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -276,12 +273,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -291,7 +287,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/TRR.html b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/TRR.html
index 2bde99ee13b..005d7b8a427 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/TRR.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/TRR.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.xdrfile.TRR &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.xdrfile.TRR &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../../index.html" />
+    <link rel="up" title="Module code" href="../../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../../index.html">
               <img class="logo" src="../../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.xdrfile.TRR</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -132,7 +129,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.TRR</h1><div class="highlight
 <span class="kn">from</span> <span class="nn">MDAnalysis</span> <span class="kn">import</span> <span class="n">NoDataError</span>
 
 
-<div class="viewcode-block" id="Timestep"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep">[docs]</a><span class="k">class</span> <span class="nc">Timestep</span><span class="p">(</span><span class="n">core</span><span class="o">.</span><span class="n">Timestep</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/TRR.html#MDAnalysis.coordinates.TRR.Timestep">[docs]</a><span class="k">class</span> <span class="nc">Timestep</span><span class="p">(</span><span class="n">core</span><span class="o">.</span><span class="n">Timestep</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Timestep for a Gromacs_ TRR trajectory.</span>
 
 <span class="sd">    TRR Timestep always has positions, velocities and forces allocated, meaning</span>
@@ -283,7 +280,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.TRR</h1><div class="highlight
         <span class="bp">self</span><span class="o">.</span><span class="n">has_forces</span> <span class="o">=</span> <span class="bp">True</span>
 
 </div>
-<div class="viewcode-block" id="TRRWriter"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter">[docs]</a><span class="k">class</span> <span class="nc">TRRWriter</span><span class="p">(</span><span class="n">core</span><span class="o">.</span><span class="n">TrjWriter</span><span class="p">):</span>
+<div class="viewcode-block" id="TRRWriter"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/TRR.html#MDAnalysis.coordinates.TRR.TRRWriter">[docs]</a><span class="k">class</span> <span class="nc">TRRWriter</span><span class="p">(</span><span class="n">core</span><span class="o">.</span><span class="n">TrjWriter</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Write a Gromacs_ TRR trajectory.</span>
 
 <span class="sd">    .. _Gromacs: http://www.gromacs.org</span>
@@ -292,7 +289,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.TRR</h1><div class="highlight
     <span class="n">units</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;time&#39;</span><span class="p">:</span> <span class="s">&#39;ps&#39;</span><span class="p">,</span> <span class="s">&#39;length&#39;</span><span class="p">:</span> <span class="s">&#39;nm&#39;</span><span class="p">,</span> <span class="s">&#39;velocity&#39;</span><span class="p">:</span> <span class="s">&#39;nm/ps&#39;</span><span class="p">,</span> <span class="s">&#39;force&#39;</span><span class="p">:</span> <span class="s">&#39;kJ/(mol*nm)&#39;</span><span class="p">}</span>
 
 </div>
-<div class="viewcode-block" id="TRRReader"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader">[docs]</a><span class="k">class</span> <span class="nc">TRRReader</span><span class="p">(</span><span class="n">core</span><span class="o">.</span><span class="n">TrjReader</span><span class="p">):</span>
+<div class="viewcode-block" id="TRRReader"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/TRR.html#MDAnalysis.coordinates.TRR.TRRReader">[docs]</a><span class="k">class</span> <span class="nc">TRRReader</span><span class="p">(</span><span class="n">core</span><span class="o">.</span><span class="n">TrjReader</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Read a Gromacs_ TRR trajectory.</span>
 
 <span class="sd">    .. versionchanged:: 0.8.0</span>
@@ -384,7 +381,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.TRR</h1><div class="highlight
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -393,12 +390,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -408,7 +404,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/XTC.html b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/XTC.html
index c6445dc8404..69cf47d6012 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/XTC.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/XTC.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.xdrfile.XTC &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.xdrfile.XTC &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../../index.html" />
+    <link rel="up" title="Module code" href="../../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../../index.html">
               <img class="logo" src="../../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.xdrfile.XTC</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -130,7 +127,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.XTC</h1><div class="highlight
 <span class="kn">from</span> <span class="nn">.core</span> <span class="kn">import</span> <span class="n">Timestep</span>
 
 
-<div class="viewcode-block" id="XTCWriter"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter">[docs]</a><span class="k">class</span> <span class="nc">XTCWriter</span><span class="p">(</span><span class="n">core</span><span class="o">.</span><span class="n">TrjWriter</span><span class="p">):</span>
+<div class="viewcode-block" id="XTCWriter"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.XTC.XTCWriter">[docs]</a><span class="k">class</span> <span class="nc">XTCWriter</span><span class="p">(</span><span class="n">core</span><span class="o">.</span><span class="n">TrjWriter</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Write a Gromacs_ XTC trajectory.</span>
 
 <span class="sd">    .. _Gromacs: http://www.gromacs.org</span>
@@ -138,7 +135,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.XTC</h1><div class="highlight
     <span class="n">format</span> <span class="o">=</span> <span class="s">&quot;XTC&quot;</span>
 
 </div>
-<div class="viewcode-block" id="XTCReader"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader">[docs]</a><span class="k">class</span> <span class="nc">XTCReader</span><span class="p">(</span><span class="n">core</span><span class="o">.</span><span class="n">TrjReader</span><span class="p">):</span>
+<div class="viewcode-block" id="XTCReader"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.XTC.XTCReader">[docs]</a><span class="k">class</span> <span class="nc">XTCReader</span><span class="p">(</span><span class="n">core</span><span class="o">.</span><span class="n">TrjReader</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Read Gromacs_ XTC trajectory.</span>
 
 <span class="sd">    .. _Gromacs: http://www.gromacs.org</span>
@@ -196,7 +193,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.XTC</h1><div class="highlight
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -205,12 +202,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -220,7 +216,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/core.html b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/core.html
index 1bb7830d016..5b424f2a8c5 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/core.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/core.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.xdrfile.core &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.xdrfile.core &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../../index.html" />
+    <link rel="up" title="Module code" href="../../../index.html" /> 
   </head>
-  <body>
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &raquo;</li> 
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../../index.html">
               <img class="logo" src="../../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -150,6 +147,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
 <span class="kn">import</span> <span class="nn">sys</span>
 <span class="kn">import</span> <span class="nn">cPickle</span>
 <span class="kn">import</span> <span class="nn">warnings</span>
+<span class="kn">import</span> <span class="nn">weakref</span>
 
 <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">libxdrfile2</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis.coordinates</span> <span class="kn">import</span> <span class="n">base</span>
@@ -159,7 +157,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
 
 
 <span class="c"># This is the XTC class. The TRR overrides with it&#39;s own.</span>
-<div class="viewcode-block" id="Timestep"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.Timestep">[docs]</a><span class="k">class</span> <span class="nc">Timestep</span><span class="p">(</span><span class="n">base</span><span class="o">.</span><span class="n">Timestep</span><span class="p">):</span>
+<div class="viewcode-block" id="Timestep"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.TRR.Timestep">[docs]</a><span class="k">class</span> <span class="nc">Timestep</span><span class="p">(</span><span class="n">base</span><span class="o">.</span><span class="n">Timestep</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Timestep for a Gromacs trajectory.</span>
 
 <span class="sd">    .. versionchanged:: 0.11.0</span>
@@ -193,11 +191,11 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
         <span class="k">return</span> <span class="n">triclinic_box</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">)</span>
 
     <span class="nd">@dimensions.setter</span>
-<div class="viewcode-block" id="Timestep.dimensions"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.Timestep.dimensions">[docs]</a>    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_unitcell</span> <span class="o">=</span> <span class="n">triclinic_vectors</span><span class="p">(</span><span class="n">box</span><span class="p">)</span>
 
-</div></div>
-<div class="viewcode-block" id="TrjWriter"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjWriter">[docs]</a><span class="k">class</span> <span class="nc">TrjWriter</span><span class="p">(</span><span class="n">base</span><span class="o">.</span><span class="n">Writer</span><span class="p">):</span>
+</div>
+<div class="viewcode-block" id="TrjWriter"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.TRR.TrjWriter">[docs]</a><span class="k">class</span> <span class="nc">TrjWriter</span><span class="p">(</span><span class="n">base</span><span class="o">.</span><span class="n">Writer</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Writes to a Gromacs trajectory file</span>
 
 <span class="sd">    (Base class)</span>
@@ -273,7 +271,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">format</span> <span class="o">==</span> <span class="s">&#39;TRR&#39;</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_emptyarr</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
 
-<div class="viewcode-block" id="TrjWriter.write_next_timestep"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjWriter.write_next_timestep">[docs]</a>    <span class="k">def</span> <span class="nf">write_next_timestep</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ts</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+<div class="viewcode-block" id="TrjWriter.write_next_timestep"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.TRR.TrjWriter.write_next_timestep">[docs]</a>    <span class="k">def</span> <span class="nf">write_next_timestep</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ts</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot; write a new timestep to the trj file</span>
 
 <span class="sd">        *ts* is a :class:`Timestep` instance containing coordinates to</span>
@@ -381,12 +379,12 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
             <span class="bp">self</span><span class="o">.</span><span class="n">xdrfile</span> <span class="o">=</span> <span class="bp">None</span>
         <span class="k">return</span> <span class="n">status</span>
 
-<div class="viewcode-block" id="TrjWriter.convert_dimensions_to_unitcell"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjWriter.convert_dimensions_to_unitcell">[docs]</a>    <span class="k">def</span> <span class="nf">convert_dimensions_to_unitcell</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ts</span><span class="p">):</span>
+<div class="viewcode-block" id="TrjWriter.convert_dimensions_to_unitcell"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.TRR.TrjWriter.convert_dimensions_to_unitcell">[docs]</a>    <span class="k">def</span> <span class="nf">convert_dimensions_to_unitcell</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ts</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Read dimensions from timestep *ts* and return Gromacs box vectors&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">convert_pos_to_native</span><span class="p">(</span><span class="n">triclinic_vectors</span><span class="p">(</span><span class="n">ts</span><span class="o">.</span><span class="n">dimensions</span><span class="p">))</span>
 
 </div></div>
-<div class="viewcode-block" id="TrjReader"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjReader">[docs]</a><span class="k">class</span> <span class="nc">TrjReader</span><span class="p">(</span><span class="n">base</span><span class="o">.</span><span class="n">Reader</span><span class="p">):</span>
+<div class="viewcode-block" id="TrjReader"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.TRR.TrjReader">[docs]</a><span class="k">class</span> <span class="nc">TrjReader</span><span class="p">(</span><span class="n">base</span><span class="o">.</span><span class="n">Reader</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Generic base class for reading Gromacs trajectories inside MDAnalysis.</span>
 
 <span class="sd">    Derive classes and set :attr:`TrjReader.format`, :attr:`TrjReader._read_trj` and :attr:`TrjReader._read_trj_atoms`.</span>
@@ -431,6 +429,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
 <span class="sd">           New keyword *refresh_offsets*</span>
 <span class="sd">        .. versionchanged:: 0.11.0</span>
 <span class="sd">           Renamed &quot;delta&quot; attribute to &quot;dt&quot;</span>
+<span class="sd">           Now passes weakref of self to ts (as &quot;_reader&quot;)</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="nb">super</span><span class="p">(</span><span class="n">TrjReader</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_cache</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
@@ -485,6 +484,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
         <span class="c"># at this time, _trr_n_atoms and _sub are set, so self.n_atoms has all it needs</span>
         <span class="c"># to determine number of atoms.</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">ts</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_Timestep</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span><span class="p">,</span> <span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">_ts_kwargs</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ts</span><span class="o">.</span><span class="n">_reader</span> <span class="o">=</span> <span class="n">weakref</span><span class="o">.</span><span class="n">ref</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
 
         <span class="c"># Read in the first timestep</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_read_next_timestep</span><span class="p">()</span>
@@ -494,7 +494,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
             <span class="bp">self</span><span class="o">.</span><span class="n">_retrieve_offsets</span><span class="p">()</span>
 
     <span class="nd">@property</span>
-<div class="viewcode-block" id="TrjReader.n_atoms"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjReader.n_atoms">[docs]</a>    <span class="k">def</span> <span class="nf">n_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">n_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;The number of publically available atoms that this reader will store in the timestep.</span>
 
 <span class="sd">        If &#39;sub&#39; was not given in the ctor, then this value will just be the actual</span>
@@ -504,9 +504,9 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
 <span class="sd">        If for any reason the trajectory cannot be read then a negative value is returned.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_sub</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sub</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">_trr_n_atoms</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="TrjReader.n_frames"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjReader.n_frames">[docs]</a>    <span class="k">def</span> <span class="nf">n_frames</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">n_frames</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Read the number of frames from the trajectory.</span>
 
 <span class="sd">        The result is cached. If for any reason the trajectory cannot</span>
@@ -528,7 +528,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
             <span class="k">return</span> <span class="mi">0</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_frames</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">offsets</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_offsets</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
@@ -541,14 +541,13 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
         <span class="k">else</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_offsets</span>
 
-    <span class="nd">@property</span>
-    <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;dt&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="TrjReader.dt"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjReader.dt">[docs]</a>    <span class="k">def</span> <span class="nf">dt</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">_get_dt</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Time step length in ps.</span>
 
 <span class="sd">        The result is computed from the trajectory and cached. If for</span>
 <span class="sd">        any reason the trajectory cannot be read then 0 is returned.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">curr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ts</span><span class="o">.</span><span class="n">frame</span>
         <span class="c"># no need for conversion: it&#39;s alread in our base unit ps</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="n">t0</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ts</span><span class="o">.</span><span class="n">time</span>
@@ -559,8 +558,8 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
         <span class="k">except</span> <span class="ne">IOError</span><span class="p">:</span>
             <span class="k">return</span> <span class="mi">0</span>
         <span class="k">finally</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">rewind</span><span class="p">()</span>
-</div>
+            <span class="bp">self</span><span class="p">[</span><span class="n">curr</span><span class="p">]</span>
+
     <span class="k">def</span> <span class="nf">_offset_filename</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="n">head</span><span class="p">,</span> <span class="n">tail</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">head</span><span class="p">,</span> <span class="s">&#39;.{0}_offsets.pkl&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">tail</span><span class="p">))</span>
@@ -588,7 +587,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
         <span class="k">except</span> <span class="ne">IOError</span><span class="p">:</span>
             <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s">&quot;Offsets could not be retrieved; they will be rebuilt instead.&quot;</span><span class="p">)</span>
 
-<div class="viewcode-block" id="TrjReader.save_offsets"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets">[docs]</a>    <span class="k">def</span> <span class="nf">save_offsets</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
+<div class="viewcode-block" id="TrjReader.save_offsets"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.TRR.TrjReader.save_offsets">[docs]</a>    <span class="k">def</span> <span class="nf">save_offsets</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Saves current trajectory offsets into *filename*, as a pickled object.</span>
 
 <span class="sd">        Along with the offsets themselves, the ctime and file size of the</span>
@@ -625,7 +624,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
         <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
             <span class="n">cPickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">output</span><span class="p">,</span> <span class="n">f</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="TrjReader.load_offsets"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjReader.load_offsets">[docs]</a>    <span class="k">def</span> <span class="nf">load_offsets</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
+<div class="viewcode-block" id="TrjReader.load_offsets"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.TRR.TrjReader.load_offsets">[docs]</a>    <span class="k">def</span> <span class="nf">load_offsets</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Loads current trajectory offsets from pickled *filename*. </span>
 
 <span class="sd">        Checks if ctime and size of trajectory file matches that stored in</span>
@@ -711,7 +710,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
             <span class="bp">self</span><span class="o">.</span><span class="n">_offsets</span> <span class="o">=</span> <span class="bp">None</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_n_frames</span> <span class="o">=</span> <span class="bp">None</span>
 </div>
-<div class="viewcode-block" id="TrjReader.open_trajectory"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjReader.open_trajectory">[docs]</a>    <span class="k">def</span> <span class="nf">open_trajectory</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="TrjReader.open_trajectory"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.TRR.TrjReader.open_trajectory">[docs]</a>    <span class="k">def</span> <span class="nf">open_trajectory</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Open xdr trajectory file.</span>
 
 <span class="sd">        :Returns: pointer to XDRFILE (and sets self.xdrfile)</span>
@@ -736,14 +735,14 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
         <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;lmbda&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">xdrfile</span>
 </div>
-<div class="viewcode-block" id="TrjReader.close"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjReader.close">[docs]</a>    <span class="k">def</span> <span class="nf">close</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="TrjReader.close"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.TRR.TrjReader.close">[docs]</a>    <span class="k">def</span> <span class="nf">close</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Close xdr trajectory file if it was open.&quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">xdrfile</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
             <span class="k">return</span>
         <span class="n">libxdrfile2</span><span class="o">.</span><span class="n">xdrfile_close</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">xdrfile</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">xdrfile</span> <span class="o">=</span> <span class="bp">None</span>  <span class="c"># guard against  crashing with a double-free pointer</span>
 </div>
-<div class="viewcode-block" id="TrjReader.Writer"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjReader.Writer">[docs]</a>    <span class="k">def</span> <span class="nf">Writer</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="TrjReader.Writer"><a class="viewcode-back" href="../../../../documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.TRR.TrjReader.Writer">[docs]</a>    <span class="k">def</span> <span class="nf">Writer</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Returns a Gromacs TrjWriter for *filename* with the same parameters as this trajectory.</span>
 
 <span class="sd">        All values can be changed through keyword arguments.</span>
@@ -842,7 +841,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.core</h1><div class="highligh
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -851,12 +850,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -866,7 +864,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html
index 80e7e73a385..c40aad8d2b3 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.coordinates.xdrfile.libxdrfile2 &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.coordinates.xdrfile.libxdrfile2 &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../../index.html" />
+    <link rel="up" title="Module code" href="../../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../../index.html">
               <img class="logo" src="../../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.coordinates.xdrfile.libxdrfile2</h1><div class="highlight"><pre>
 <span class="c"># coding=utf-8</span>
@@ -634,7 +631,7 @@ <h1>Source code for MDAnalysis.coordinates.xdrfile.libxdrfile2</h1><div class="h
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -643,12 +640,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -658,7 +654,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/core/AtomGroup.html b/package/doc/html/_modules/MDAnalysis/core/AtomGroup.html
index 17158078838..94cb2b62c2a 100644
--- a/package/doc/html/_modules/MDAnalysis/core/AtomGroup.html
+++ b/package/doc/html/_modules/MDAnalysis/core/AtomGroup.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.core.AtomGroup &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.core.AtomGroup &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -161,33 +158,36 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 
 <span class="sd">will typically work as expected. When working with collections such as</span>
 <span class="sd">:class:`AtomGroup` or :class:`ResidueGroup` it is generally better to use</span>
-<span class="sd">provided setter methods such as :meth:`AtomGroup.set_resname` or</span>
-<span class="sd">:meth:`ResidueGroup.set_resname`.</span>
+<span class="sd">properties such as :attr:`AtomGroup.resnames` or :attr:`ResidueGroup.resnames`</span>
+<span class="sd">to modify their items&#39; attributes.</span>
 
-<span class="sd">There are two cases when it is very important to use the setters:</span>
+<span class="sd">There are two cases when it is very important to use these collective</span>
+<span class="sd">properties:</span>
 
-<span class="sd">* changing *resid*: :meth:`AtomGroup.set_resid` and :meth:`ResidueGroup.set_resid`</span>
-<span class="sd">* changing *segid*: :meth:`AtomGroup.set_segid` and :meth:`ResidueGroup.set_segid`</span>
+<span class="sd">* changing *resid*: :attr:`AtomGroup.resids` and :attr:`ResidueGroup.resids`</span>
+<span class="sd">* changing *segid*: :attr:`AtomGroup.segids` and :attr:`ResidueGroup.segids`</span>
 
 <span class="sd">Because residues are determined by the :attr:`Atom.resid` and segments by</span>
-<span class="sd">:attr:`Atom.segid`, the above methods take extra care to rebuild the list of</span>
-<span class="sd">segments and residues.</span>
+<span class="sd">:attr:`Atom.segid`, the above properties take extra care to rebuild the list of</span>
+<span class="sd">segments and residues. Alternatively, the same effect can be obtained using</span>
+<span class="sd">the corresponding setter method, e.g. :meth:`AtomGroup.set_resids`.</span>
 
 <span class="sd">.. Note::</span>
 
-<span class="sd">   :meth:`AtomGroup.set_resid`, :meth:`ResidueGroup.set_resid`,</span>
-<span class="sd">   :meth:`AtomGroup.set_segid`, :meth:`ResidueGroup.set_segid` can change the</span>
-<span class="sd">   topology: they can split or merge residues or segments.</span>
+<span class="sd">   Setting any of</span>
+<span class="sd">   :attr:`AtomGroup.resids`, :attr:`ResidueGroup.resids`,</span>
+<span class="sd">   :attr:`AtomGroup.segids`, :attr:`ResidueGroup.segids` </span>
+<span class="sd">   can change the topology: they can split or merge residues or segments.</span>
 
 <span class="sd">Splitting/merging of residues is probably not very useful because no chemical</span>
 <span class="sd">rearrangements are carried out. Manipulating segments might be more useful in</span>
 <span class="sd">order to add additional structure to a :class:`Universe` and provide instant</span>
 <span class="sd">segment selectors for interactive work::</span>
 
-<span class="sd">  u.select_atoms(&quot;protein&quot;).set_segid(&quot;protein&quot;)</span>
-<span class="sd">  u.select_atoms(&quot;resname POPE or resname POPC&quot;).set_segid(&quot;lipids&quot;)</span>
-<span class="sd">  u.select_atoms(&quot;resname SOL&quot;).set_segid(&quot;water&quot;)</span>
-<span class="sd">  u.select_atoms(&quot;resname NA or resname CL&quot;).set_segid(&quot;ions&quot;)</span>
+<span class="sd">  u.select_atoms(&quot;protein&quot;).set_segids(&quot;protein&quot;)</span>
+<span class="sd">  u.select_atoms(&quot;resname POPE or resname POPC&quot;).set_segids(&quot;lipids&quot;)</span>
+<span class="sd">  u.select_atoms(&quot;resname SOL&quot;).set_segids(&quot;water&quot;)</span>
+<span class="sd">  u.select_atoms(&quot;resname NA or resname CL&quot;).set_segids(&quot;ions&quot;)</span>
 
 <span class="sd">  u.protein.n_residues</span>
 <span class="sd">  water_oxygens = u.water.OW</span>
@@ -199,15 +199,15 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">store the canonical residue IDs (&quot;resnum&quot;) one could the use ::</span>
 
 <span class="sd">  protein = u.select_atoms(&quot;protein&quot;).residues</span>
-<span class="sd">  protein.set_resnum(protein.resnums + 9)</span>
+<span class="sd">  protein.set_resnums(protein.resnums + 9)</span>
 
 <span class="sd">One can then use ``protein.select(&quot;resnum 42&quot;)`` to select the residue that has</span>
 <span class="sd">the canonical residue id 42 (instead of ``resid 33``).</span>
 
-<span class="sd">One can also read the resids directly from  an original PDB file::</span>
+<span class="sd">One can also read the resids directly from an original PDB file::</span>
 
 <span class="sd">  orig = MDAnalysis.Universe(&quot;2jln.pdb&quot;)</span>
-<span class="sd">  protein.set_resnum(orig.select_atoms(&quot;protein&quot;).resids)</span>
+<span class="sd">  protein.set_resnums(orig.select_atoms(&quot;protein&quot;).resids)</span>
 
 
 <span class="sd">Working with Topologies</span>
@@ -248,11 +248,11 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">     (&#39;C&#39;, &#39;C&#39;, &#39;O&#39;),</span>
 <span class="sd">     (&#39;H&#39;, &#39;C&#39;, &#39;O&#39;)]</span>
 
-<span class="sd">There is only C-C-H bonds and no H-C-C bonds.  Selection however is</span>
+<span class="sd">There are only C-C-H bonds and no H-C-C bonds.  Selection however is</span>
 <span class="sd">aware that sometimes types are reversed::</span>
 
-<span class="sd">    u.angles.select_bonds((&#39;H&#39;, &#39;C&#39;, &#39;C&#39;))  # note reversal of type</span>
-<span class="sd">    &gt;&gt;&gt; &lt;TopologyGroup containing 7365 Angles&gt;</span>
+<span class="sd">    &gt;&gt;&gt; u.angles.select_bonds((&#39;H&#39;, &#39;C&#39;, &#39;C&#39;))  # note reversal of type</span>
+<span class="sd">    &lt;TopologyGroup containing 7365 Angles&gt;</span>
 
 <span class="sd">TopologyGroups can be combined and indexed::</span>
 
@@ -466,7 +466,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">.. autoclass:: SegmentGroup</span>
 <span class="sd">   :members:</span>
 
-<span class="sd">.. autofunction:: asUniverse</span>
+<span class="sd">.. autofunction:: as_Universe</span>
 <span class="sd">.. autoexception:: SelectionError</span>
 <span class="sd">   :no-members:</span>
 <span class="sd">.. autoexception:: SelectionWarning</span>
@@ -613,12 +613,12 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
             <span class="k">return</span> <span class="n">AtomGroup</span><span class="p">([</span><span class="bp">self</span><span class="p">]</span> <span class="o">+</span> <span class="n">other</span><span class="o">.</span><span class="n">_atoms</span><span class="p">)</span>
 
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Atom.number"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.number">[docs]</a>    <span class="k">def</span> <span class="nf">number</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">number</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;The index of this atom&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Atom.pos"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.pos">[docs]</a>    <span class="k">def</span> <span class="nf">pos</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">pos</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;coordinates of the atom</span>
 
 <span class="sd">        Get the current cartesian coordinates of the atom (read-only).</span>
@@ -627,7 +627,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">           use :attr:`position`</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">position</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">position</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;coordinates of the atom</span>
@@ -639,14 +639,14 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">positions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">]</span>  <span class="c"># internal numbering starts at 0</span>
 
     <span class="nd">@position.setter</span>
-<div class="viewcode-block" id="Atom.position"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.position">[docs]</a>    <span class="k">def</span> <span class="nf">position</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">coords</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">position</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">coords</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Set the current cartesian coordinates of the atom.</span>
 <span class="sd">        @param coords: a 1x3 numpy array of {x,y,z} coordinates, or optionally</span>
 <span class="sd">            a single scalar if you should want to set all coordinates to the same value.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">positions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="p">:]</span> <span class="o">=</span> <span class="n">coords</span>  <span class="c"># internal numbering starts at 0</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">velocity</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Current velocity of the atom.</span>
@@ -666,7 +666,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="n">NoDataError</span><span class="p">(</span><span class="s">&quot;Timestep does not contain velocities&quot;</span><span class="p">)</span>
 
     <span class="nd">@velocity.setter</span>
-<div class="viewcode-block" id="Atom.velocity"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.velocity">[docs]</a>    <span class="k">def</span> <span class="nf">velocity</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vals</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">velocity</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vals</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Set the current velocity of the atom.</span>
 
 <span class="sd">        A :exc:`~MDAnalysis.NoDataError` is raised if the trajectory</span>
@@ -678,7 +678,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">velocities</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">]</span> <span class="o">=</span> <span class="n">vals</span>
         <span class="k">except</span> <span class="p">(</span><span class="ne">AttributeError</span><span class="p">,</span> <span class="n">NoDataError</span><span class="p">):</span>
             <span class="k">raise</span> <span class="n">NoDataError</span><span class="p">(</span><span class="s">&quot;Timestep does not contain velocities&quot;</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">force</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Current force of the atom.</span>
@@ -696,7 +696,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="n">NoDataError</span><span class="p">(</span><span class="s">&quot;Timestep does not contain forces&quot;</span><span class="p">)</span>
 
     <span class="nd">@force.setter</span>
-<div class="viewcode-block" id="Atom.force"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.force">[docs]</a>    <span class="k">def</span> <span class="nf">force</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vals</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">force</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vals</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Set the current force of the atom.</span>
 
 <span class="sd">        .. versionadded:: 0.9.2</span>
@@ -705,7 +705,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">forces</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">]</span> <span class="o">=</span> <span class="n">vals</span>
         <span class="k">except</span> <span class="p">(</span><span class="ne">AttributeError</span><span class="p">,</span> <span class="n">NoDataError</span><span class="p">):</span>
             <span class="k">raise</span> <span class="n">NoDataError</span><span class="p">(</span><span class="s">&quot;Timestep does not contain forces&quot;</span><span class="p">)</span>
-</div>
+
 <div class="viewcode-block" id="Atom.centroid"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.centroid">[docs]</a>    <span class="k">def</span> <span class="nf">centroid</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;The centroid of an atom is its position, :attr:`Atom.position`.&quot;&quot;&quot;</span>
         <span class="c"># centroid exists for compatibility with AtomGroup</span>
@@ -722,12 +722,12 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
                 <span class="s">&quot;Atom {0} is not assigned to a Universe&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">))</span>
 
     <span class="nd">@universe.setter</span>
-<div class="viewcode-block" id="Atom.universe"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.universe">[docs]</a>    <span class="k">def</span> <span class="nf">universe</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">universe</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">):</span>
         <span class="c"># Beware: Atoms hold only weakrefs to the universe</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_universe</span> <span class="o">=</span> <span class="n">weakref</span><span class="o">.</span><span class="n">ref</span><span class="p">(</span><span class="n">universe</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Atom.bonded_atoms"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.bonded_atoms">[docs]</a>    <span class="k">def</span> <span class="nf">bonded_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">bonded_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;An AtomGroup of the Atoms that this Atom is bonded to.</span>
 
 <span class="sd">        .. versionadded:: 0.9</span>
@@ -735,35 +735,35 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">AtomGroup</span><span class="p">([</span><span class="n">b</span><span class="o">.</span><span class="n">partner</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="p">])</span>
 
     <span class="c"># The following look up a dictionary stored in the Universe.</span>
-    <span class="c"># These dictionaries are lazily built</span></div>
+    <span class="c"># These dictionaries are lazily built</span>
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Atom.fragment"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.fragment">[docs]</a>    <span class="k">def</span> <span class="nf">fragment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">fragment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;The fragment that this Atom is part of</span>
 
 <span class="sd">        .. versionadded:: 0.9.0</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">_fragmentDict</span><span class="p">[</span><span class="bp">self</span><span class="p">]</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Atom.bonds"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.bonds">[docs]</a>    <span class="k">def</span> <span class="nf">bonds</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">bonds</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;A TopologyGroup of the bonds that this Atom is in</span>
 
 <span class="sd">        .. versionchanged:: 0.9.0</span>
 <span class="sd">           Changed to managed property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">TopologyGroup</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">_bondDict</span><span class="p">[</span><span class="bp">self</span><span class="p">])</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Atom.angles"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.angles">[docs]</a>    <span class="k">def</span> <span class="nf">angles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">angles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;A TopologyGroup of the angles that this Atom is in</span>
 
 <span class="sd">        .. versionchanged:: 0.9.0</span>
 <span class="sd">           Changed to managed property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">TopologyGroup</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">_angleDict</span><span class="p">[</span><span class="bp">self</span><span class="p">])</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Atom.dihedrals"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.dihedrals">[docs]</a>    <span class="k">def</span> <span class="nf">dihedrals</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dihedrals</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;A TopologyGroup of the dihedrals that this Atom is in</span>
 
 <span class="sd">        .. versionchanged:: 0.9.0</span>
@@ -772,9 +772,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">           Renamed to dihedrals (was torsions)</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">TopologyGroup</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">_dihedralDict</span><span class="p">[</span><span class="bp">self</span><span class="p">])</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Atom.impropers"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.impropers">[docs]</a>    <span class="k">def</span> <span class="nf">impropers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">impropers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;A TopologyGroup of the improper dihedrals that this Atom is in</span>
 
 <span class="sd">        .. versionchanged:: 0.9.0</span>
@@ -782,7 +782,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">TopologyGroup</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">_improperDict</span><span class="p">[</span><span class="bp">self</span><span class="p">])</span>
 
-</div></div>
+</div>
 <div class="viewcode-block" id="AtomGroup"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup">[docs]</a><span class="k">class</span> <span class="nc">AtomGroup</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;A group of atoms.</span>
 
@@ -881,6 +881,10 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">       The ``bond``, ``angle``, ``dihedral`` and ``improper`` methods were removed and replaced</span>
 <span class="sd">       with properties of the same name which return the corresponding object.</span>
 <span class="sd">       Deprecated ``selectAtoms`` in favour of ``select_atoms``.</span>
+<span class="sd">       Setters are now plural to match property names.</span>
+<span class="sd">       Properties referring to residue (``resids``, ``resnames``, ``resnums``)</span>
+<span class="sd">       or segment [``segids``] properties now yield arrays of length equal to</span>
+<span class="sd">       ``n_atoms``</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="c"># for generalized __getitem__ __iter__ and __len__</span>
     <span class="c"># (override _containername for ResidueGroup and SegmentGroup)</span>
@@ -1001,7 +1005,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
     <span class="c"># between AtomGroup, Residue, ResidueGroup, Segment; access the list as</span>
     <span class="c"># _atoms (although atoms supports all list-like operations, too).</span></div>
     <span class="nd">@property</span>
-<div class="viewcode-block" id="AtomGroup.atoms"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.atoms">[docs]</a>    <span class="k">def</span> <span class="nf">atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;:class:`AtomGroup` of all atoms in this group.</span>
 
 <span class="sd">        If this is a :class:`AtomGroup` then it returns itself. Otherwise, it</span>
@@ -1015,21 +1019,21 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">==</span> <span class="n">AtomGroup</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span>
         <span class="k">return</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__atoms</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="AtomGroup._atoms"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup._atoms">[docs]</a>    <span class="k">def</span> <span class="nf">_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;a immutable list of references to the atoms in the group&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__atoms</span>
 
-    <span class="c"># Universe pointer is important for Selections to work on groups</span></div>
+    <span class="c"># Universe pointer is important for Selections to work on groups</span>
     <span class="nd">@property</span>
-<div class="viewcode-block" id="AtomGroup.universe"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.universe">[docs]</a>    <span class="k">def</span> <span class="nf">universe</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">universe</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;The universe to which the atoms belong (read-only).&quot;&quot;&quot;</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">universe</span>
         <span class="k">except</span> <span class="p">(</span><span class="ne">AttributeError</span><span class="p">,</span> <span class="ne">IndexError</span><span class="p">):</span>
             <span class="k">return</span> <span class="bp">None</span>
-</div>
+
     <span class="k">def</span> <span class="nf">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Number of atoms in the group&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_container</span><span class="p">)</span>
@@ -1146,23 +1150,23 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
                         <span class="o">*</span><span class="n">state</span><span class="p">[</span><span class="mi">2</span><span class="p">:]))</span>
 
     <span class="nd">@property</span>
-<div class="viewcode-block" id="AtomGroup.n_atoms"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.n_atoms">[docs]</a>    <span class="k">def</span> <span class="nf">n_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">n_atoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Total number of atoms in the group&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="AtomGroup.n_residues"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.n_residues">[docs]</a>    <span class="k">def</span> <span class="nf">n_residues</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">n_residues</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Total number of residues in the group&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="AtomGroup.n_segments"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.n_segments">[docs]</a>    <span class="k">def</span> <span class="nf">n_segments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">n_segments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Total number of segments in the group&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">segments</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;indices&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="AtomGroup.indices"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.indices">[docs]</a>    <span class="k">def</span> <span class="nf">indices</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">indices</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Array of all :attr:`Atom.index` in the group.</span>
 
 <span class="sd">        These indices are 0-based and can be used to directly index</span>
@@ -1176,7 +1180,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">           Now a property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">atom</span><span class="o">.</span><span class="n">index</span> <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;masses&#39;</span><span class="p">)</span>
     <span class="k">def</span> <span class="nf">masses</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -1188,14 +1192,16 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">atom</span><span class="o">.</span><span class="n">mass</span> <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@masses.setter</span>
-<div class="viewcode-block" id="AtomGroup.masses"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.masses">[docs]</a>    <span class="k">def</span> <span class="nf">masses</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">masses</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_clear_caches</span><span class="p">(</span><span class="s">&#39;masses&#39;</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_mass</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
-<div class="viewcode-block" id="AtomGroup.totalMass"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.totalMass">[docs]</a>    <span class="k">def</span> <span class="nf">totalMass</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_masses</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.total_mass"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.total_mass">[docs]</a>    <span class="k">def</span> <span class="nf">total_mass</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Total mass of the selection (masses are taken from the topology or guessed).&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">masses</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
 </div>
+    <span class="n">totalMass</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">total_mass</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;totalMass&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;total_mass&#39;</span><span class="p">)</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">charges</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Array of partial charges of the atoms (as defined in the topology)</span>
@@ -1206,16 +1212,18 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">atom</span><span class="o">.</span><span class="n">charge</span> <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@charges.setter</span>
-<div class="viewcode-block" id="AtomGroup.charges"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.charges">[docs]</a>    <span class="k">def</span> <span class="nf">charges</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_charge</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
-<div class="viewcode-block" id="AtomGroup.totalCharge"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.totalCharge">[docs]</a>    <span class="k">def</span> <span class="nf">totalCharge</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">charges</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_charges</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.total_charge"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.total_charge">[docs]</a>    <span class="k">def</span> <span class="nf">total_charge</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Sum of all partial charges (must be defined in topology).&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">charges</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
 </div>
+    <span class="n">totalCharge</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">total_charge</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;totalCharge&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;total_charge&#39;</span><span class="p">)</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">names</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Returns a list of atom names.</span>
+        <span class="sd">&quot;&quot;&quot;Returns an array of atom names.</span>
 
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Returns a :class:`numpy.ndarray`</span>
@@ -1225,9 +1233,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@names.setter</span>
-<div class="viewcode-block" id="AtomGroup.names"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.names">[docs]</a>    <span class="k">def</span> <span class="nf">names</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_name</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
+    <span class="k">def</span> <span class="nf">names</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_names</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">types</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Returns an array of atom types.</span>
@@ -1239,9 +1247,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">type</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@types.setter</span>
-<div class="viewcode-block" id="AtomGroup.types"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.types">[docs]</a>    <span class="k">def</span> <span class="nf">types</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_type</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
+    <span class="k">def</span> <span class="nf">types</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_types</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">radii</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Array of atomic radii (as defined in the PQR file)</span>
@@ -1252,9 +1260,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">atom</span><span class="o">.</span><span class="n">radius</span> <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@radii.setter</span>
-<div class="viewcode-block" id="AtomGroup.radii"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.radii">[docs]</a>    <span class="k">def</span> <span class="nf">radii</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_radius</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
+    <span class="k">def</span> <span class="nf">radii</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_radii</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">bfactors</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Crystallographic B-factors (from PDB) in A**2.</span>
@@ -1262,9 +1270,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">atom</span><span class="o">.</span><span class="n">bfactor</span> <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@bfactors.setter</span>
-<div class="viewcode-block" id="AtomGroup.bfactors"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.bfactors">[docs]</a>    <span class="k">def</span> <span class="nf">bfactors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_bfactor</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
+    <span class="k">def</span> <span class="nf">bfactors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_bfactors</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">altLocs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;numpy array of the altLocs for all atoms in this group</span>
@@ -1274,9 +1282,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">atom</span><span class="o">.</span><span class="n">altLoc</span> <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@altLocs.setter</span>
-<div class="viewcode-block" id="AtomGroup.altLocs"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.altLocs">[docs]</a>    <span class="k">def</span> <span class="nf">altLocs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_altloc</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
+    <span class="k">def</span> <span class="nf">altLocs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_altlocs</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">serials</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;numpy array of the serials for all atoms in this group</span>
@@ -1286,12 +1294,12 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">atom</span><span class="o">.</span><span class="n">serial</span> <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@serials.setter</span>
-<div class="viewcode-block" id="AtomGroup.serials"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.serials">[docs]</a>    <span class="k">def</span> <span class="nf">serials</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_serial</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
+    <span class="k">def</span> <span class="nf">serials</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_serials</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;residues&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="AtomGroup.residues"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.residues">[docs]</a>    <span class="k">def</span> <span class="nf">residues</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">residues</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Read-only list of :class:`Residue` objects.</span>
 
 <span class="sd">        A :class:`ResidueGroup` of all residues that contain atoms in</span>
@@ -1310,10 +1318,10 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
                 <span class="n">seen_residues</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">atom</span><span class="o">.</span><span class="n">residue</span><span class="p">)</span>
             <span class="n">current_residue</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">residue</span>
         <span class="k">return</span> <span class="n">ResidueGroup</span><span class="p">(</span><span class="n">residues</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;segments&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="AtomGroup.segments"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.segments">[docs]</a>    <span class="k">def</span> <span class="nf">segments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">segments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Read-only list of :class:`Segment` objects.</span>
 
 <span class="sd">        A :class:`SegmentGroup` of all segments that contain atoms in this group.</span>
@@ -1332,68 +1340,68 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
                 <span class="n">seen_segments</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">atom</span><span class="o">.</span><span class="n">segment</span><span class="p">)</span>
             <span class="n">current_segment</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">segment</span>
         <span class="k">return</span> <span class="n">SegmentGroup</span><span class="p">(</span><span class="n">segments</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">resids</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Returns a list of residue numbers.</span>
+        <span class="sd">&quot;&quot;&quot;Returns an array of residue numbers.</span>
 
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Returns a :class:`numpy.ndarray`</span>
 <span class="sd">        .. versionchanged:: 0.11.0</span>
-<span class="sd">           Now a property</span>
+<span class="sd">           Now a property and returns array of length `len(self)`</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">id</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">resid</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@resids.setter</span>
-<div class="viewcode-block" id="AtomGroup.resids"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.resids">[docs]</a>    <span class="k">def</span> <span class="nf">resids</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_resid</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
+    <span class="k">def</span> <span class="nf">resids</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_resids</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">resnames</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Returns a list of residue names.</span>
+        <span class="sd">&quot;&quot;&quot;Returns an array of residue names.</span>
 
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Returns a :class:`numpy.ndarray`</span>
 <span class="sd">        .. versionchanged:: 0.11.0</span>
-<span class="sd">           Now a property</span>
+<span class="sd">           Now a property and returns array of length `len(self)`</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">resname</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@resnames.setter</span>
-<div class="viewcode-block" id="AtomGroup.resnames"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.resnames">[docs]</a>    <span class="k">def</span> <span class="nf">resnames</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_resname</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
+    <span class="k">def</span> <span class="nf">resnames</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_resnames</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">resnums</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Returns a list of canonical residue numbers.</span>
+        <span class="sd">&quot;&quot;&quot;Returns an array of canonical residue numbers.</span>
 
 <span class="sd">        .. versionadded:: 0.7.4</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Returns a :class:`numpy.ndarray`</span>
 <span class="sd">        .. versionchanged:: 0.11.0</span>
-<span class="sd">           Now a property</span>
+<span class="sd">           Now a property and returns array of length `len(self)`</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">resnum</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">resnum</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@resnums.setter</span>
-<div class="viewcode-block" id="AtomGroup.resnums"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.resnums">[docs]</a>    <span class="k">def</span> <span class="nf">resnums</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_resnum</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
+    <span class="k">def</span> <span class="nf">resnums</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_resnums</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">segids</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Returns a list of segment ids (=segment names).</span>
+        <span class="sd">&quot;&quot;&quot;Returns an array of segment names.</span>
 
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Returns a :class:`numpy.ndarray`</span>
 <span class="sd">        .. versionchanged:: 0.11.0</span>
-<span class="sd">           Now a property</span>
+<span class="sd">           Now a property and returns array of length `len(self)`</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">s</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">segments</span><span class="p">])</span>
+        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">segid</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">])</span>
 
     <span class="nd">@segids.setter</span>
-<div class="viewcode-block" id="AtomGroup.segids"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.segids">[docs]</a>    <span class="k">def</span> <span class="nf">segids</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_segid</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
-</div>
+    <span class="k">def</span> <span class="nf">segids</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_segids</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
 <div class="viewcode-block" id="AtomGroup.sequence"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.sequence">[docs]</a>    <span class="k">def</span> <span class="nf">sequence</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Returns the amino acid sequence.</span>
 
@@ -1489,7 +1497,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 </div>
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;fragments&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="AtomGroup.fragments"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.fragments">[docs]</a>    <span class="k">def</span> <span class="nf">fragments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">fragments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Read-only list of fragments.</span>
 
 <span class="sd">        Contains all fragments that any Atom in this AtomGroup is part of, the contents of</span>
@@ -1498,7 +1506,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">        .. versionadded 0.9.0</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">fragment</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">))</span>
-</div>
+
 <div class="viewcode-block" id="AtomGroup.guess_bonds"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.guess_bonds">[docs]</a>    <span class="k">def</span> <span class="nf">guess_bonds</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vdwradii</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Guess all the bonds that exist within this AtomGroup and add to Universe.</span>
 
@@ -1546,7 +1554,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 </div>
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;bonds&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="AtomGroup.bonds"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.bonds">[docs]</a>    <span class="k">def</span> <span class="nf">bonds</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">bonds</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;All the bonds in this AtomGroup</span>
 
 <span class="sd">        Note that these bonds might extend out of the AtomGroup, to select</span>
@@ -1560,10 +1568,10 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="n">mybonds</span> <span class="o">=</span> <span class="p">[</span><span class="n">b</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span> <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">a</span><span class="o">.</span><span class="n">bonds</span><span class="p">]</span>
 
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">TopologyGroup</span><span class="p">(</span><span class="n">mybonds</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;angles&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="AtomGroup.angles"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.angles">[docs]</a>    <span class="k">def</span> <span class="nf">angles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">angles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;All the angles in this AtomGroup</span>
 
 <span class="sd">        Note that these angles might extend out of the AtomGroup, to select</span>
@@ -1577,10 +1585,10 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="n">mybonds</span> <span class="o">=</span> <span class="p">[</span><span class="n">b</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span> <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">a</span><span class="o">.</span><span class="n">angles</span><span class="p">]</span>
 
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">TopologyGroup</span><span class="p">(</span><span class="n">mybonds</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;dihedrals&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="AtomGroup.dihedrals"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.dihedrals">[docs]</a>    <span class="k">def</span> <span class="nf">dihedrals</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dihedrals</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;All the dihedrals in this AtomGroup</span>
 
 <span class="sd">        Note that these dihedrals might extend out of the AtomGroup, to select</span>
@@ -1594,10 +1602,10 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="n">mybonds</span> <span class="o">=</span> <span class="p">[</span><span class="n">b</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span> <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">a</span><span class="o">.</span><span class="n">dihedrals</span><span class="p">]</span>
 
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">TopologyGroup</span><span class="p">(</span><span class="n">mybonds</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;impropers&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="AtomGroup.impropers"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.impropers">[docs]</a>    <span class="k">def</span> <span class="nf">impropers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">impropers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;All the improper dihedrals in this AtomGroup</span>
 
 <span class="sd">        Note that these improper dihedrals might extend out of the AtomGroup,</span>
@@ -1611,7 +1619,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="n">mybonds</span> <span class="o">=</span> <span class="p">[</span><span class="n">b</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span> <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">a</span><span class="o">.</span><span class="n">impropers</span><span class="p">]</span>
 
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">TopologyGroup</span><span class="p">(</span><span class="n">mybonds</span><span class="p">)</span>
-</div>
+
     <span class="k">def</span> <span class="nf">_set_attribute</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">groupname</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Set attribute *name* to *value* for all elements in *groupname*.</span>
 
@@ -1675,8 +1683,8 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
     <span class="c"># override for ResidueGroup, SegmentGroup accordingly</span>
     <span class="nb">set</span> <span class="o">=</span> <span class="n">_set_atoms</span>
 
-<div class="viewcode-block" id="AtomGroup.set_name"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_name">[docs]</a>    <span class="k">def</span> <span class="nf">set_name</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the atom name to string for *all atoms* in the AtomGroup.</span>
+<div class="viewcode-block" id="AtomGroup.set_names"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_names">[docs]</a>    <span class="k">def</span> <span class="nf">set_names</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the atom names to string for *all atoms* in the AtomGroup.</span>
 
 <span class="sd">        If *value* is a sequence of the same length as the :class:`AtomGroup`</span>
 <span class="sd">        then each :attr:`Atom.name` is set to the corresponding value. If</span>
@@ -1686,11 +1694,15 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">        .. versionadded:: 0.7.4</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;name&quot;</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">conversion</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.set_resid"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resid">[docs]</a>    <span class="k">def</span> <span class="nf">set_resid</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resid</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the resid to integer *resid* for **all atoms** in the :class:`AtomGroup`.</span>
+    <span class="n">set_name</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_names</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_name&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_names&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.set_resids"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resids">[docs]</a>    <span class="k">def</span> <span class="nf">set_resids</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resid</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the resids to integer *resid* for **all atoms** in the :class:`AtomGroup`.</span>
 
 <span class="sd">        If *resid* is a sequence of the same length as the :class:`AtomGroup`</span>
 <span class="sd">        then each :attr:`Atom.resid` is set to the corresponding value together</span>
@@ -1714,20 +1726,27 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">           Can set atoms and residues to distinct values by providing a</span>
 <span class="sd">           sequence or iterable and can change the topology via</span>
 <span class="sd">           :func:`MDAnalysis.topology.core.build_residues`.</span>
-
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="kn">from</span> <span class="nn">MDAnalysis.topology.core</span> <span class="kn">import</span> <span class="n">build_residues</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;resid&quot;</span><span class="p">,</span> <span class="n">resid</span><span class="p">,</span> <span class="n">conversion</span><span class="o">=</span><span class="nb">int</span><span class="p">)</span>
         <span class="c"># Note that this also automagically updates THIS AtomGroup;</span>
         <span class="c"># the side effect of build_residues(self.atoms) is to update all Atoms!!!!</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_fill_cache</span><span class="p">(</span><span class="s">&#39;residues&#39;</span><span class="p">,</span> <span class="n">build_residues</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">))</span>
-        <span class="c"># make sure to update the whole universe: the Atoms are shared but ResidueGroups are not</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_fill_cache</span><span class="p">(</span><span class="s">&#39;residues&#39;</span><span class="p">,</span> <span class="n">ResidueGroup</span><span class="p">(</span><span class="n">build_residues</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">)))</span>
+
+        <span class="c"># make sure to update the whole universe: the Atoms are shared but</span>
+        <span class="c"># ResidueGroups are not</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">_fill_cache</span><span class="p">(</span><span class="s">&#39;residues&#39;</span><span class="p">,</span> <span class="n">build_residues</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="p">))</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">_fill_cache</span><span class="p">(</span>
+                    <span class="s">&#39;residues&#39;</span><span class="p">,</span>
+                    <span class="n">ResidueGroup</span><span class="p">(</span><span class="n">build_residues</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="p">)))</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.set_resnum"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resnum">[docs]</a>    <span class="k">def</span> <span class="nf">set_resnum</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resnum</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the resnum to *resnum* for **all atoms** in the :class:`AtomGroup`.</span>
+    <span class="n">set_resid</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_resids</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_resid&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_resids&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.set_resnums"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resnums">[docs]</a>    <span class="k">def</span> <span class="nf">set_resnums</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resnum</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the resnums to *resnum* for **all atoms** in the :class:`AtomGroup`.</span>
 
 <span class="sd">        If *resnum* is a sequence of the same length as the :class:`AtomGroup`</span>
 <span class="sd">        then each :attr:`Atom.resnum` is set to the corresponding value together</span>
@@ -1747,20 +1766,15 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">           Also changes the residues.</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms and residues to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="kn">from</span> <span class="nn">MDAnalysis.topology.core</span> <span class="kn">import</span> <span class="n">build_residues</span>
-
         <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;resnum&quot;</span><span class="p">,</span> <span class="n">resnum</span><span class="p">)</span>
-        <span class="c"># build_residues() is the easiest (though expensive) way to make sure</span>
-        <span class="c"># that all residues get their new resnum. There&#39;s no easy way to parse</span>
-        <span class="c"># a per-atom resnum list (with potential duplicates) into a list of</span>
-        <span class="c"># corresponding residues.</span>
-        <span class="c">#</span>
-        <span class="c"># (This comment applies to the analogous methods below as well.)</span>
-        <span class="n">build_residues</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.set_resname"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resname">[docs]</a>    <span class="k">def</span> <span class="nf">set_resname</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resname</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the resname to string *resname* for **all atoms** in the :class:`AtomGroup`.</span>
+    <span class="n">set_resnum</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_resnums</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_resnum&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_resnums&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.set_resnames"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resnames">[docs]</a>    <span class="k">def</span> <span class="nf">set_resnames</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resname</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the resnames to string *resname* for **all atoms** in the :class:`AtomGroup`.</span>
 
 <span class="sd">        If *resname* is a sequence of the same length as the :class:`AtomGroup`</span>
 <span class="sd">        then each :attr:`Atom.resname` is set to the corresponding value together</span>
@@ -1773,14 +1787,17 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">           Also changes the residues.</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms and residues to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="kn">from</span> <span class="nn">MDAnalysis.topology.core</span> <span class="kn">import</span> <span class="n">build_residues</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;resname&quot;</span><span class="p">,</span> <span class="n">resname</span><span class="p">,</span> <span class="n">conversion</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
-        <span class="n">build_residues</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.set_segid"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_segid">[docs]</a>    <span class="k">def</span> <span class="nf">set_segid</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">segid</span><span class="p">,</span> <span class="n">buildsegments</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the segid to *segid* for all atoms in the :class:`AtomGroup`.</span>
+    <span class="n">set_resname</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_resnames</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_resname&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_resnames&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.set_segids"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_segids">[docs]</a>    <span class="k">def</span> <span class="nf">set_segids</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">segid</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the segids to *segid* for all atoms in the :class:`AtomGroup`.</span>
 
 <span class="sd">        If *segid* is a sequence of the same length as the :class:`AtomGroup`</span>
 <span class="sd">        then each :attr:`Atom.segid` is set to the corresponding value together</span>
@@ -1792,95 +1809,154 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 
 <span class="sd">           :meth:`set_segid` can change the topology.</span>
 
-<span class="sd">           With the default *buildsegments* = ``True`` it can be used to join</span>
-<span class="sd">           segments or to break groups into multiple disjoint segments. Note</span>
-<span class="sd">           that each :class:`Atom` can only belong to a single</span>
-<span class="sd">           :class:`Segment`.</span>
-
-<span class="sd">        For performance reasons, *buildsegments* can be set to ``False``. Then</span>
-<span class="sd">        one needs to run :meth:`Universe._build_segments` manually later in</span>
-<span class="sd">        order to update the list of :class:`Segment` instances and regenerate</span>
-<span class="sd">        the segid instant selectors.</span>
-
 <span class="sd">        .. versionadded:: 0.7.4</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms and residues to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Stale caches are problematic; though it can be expensive, changing segid</span>
+<span class="sd">           results in Segments being regenerated</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;segid&quot;</span><span class="p">,</span> <span class="n">segid</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_clear_caches</span><span class="p">(</span><span class="s">&#39;segments&#39;</span><span class="p">)</span>
-        <span class="k">if</span> <span class="n">buildsegments</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">_build_segments</span><span class="p">()</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="c"># do not even update the local segment</span>
-            <span class="k">pass</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">_clear_caches</span><span class="p">(</span><span class="s">&#39;segments&#39;</span><span class="p">)</span>
+        <span class="kn">from</span> <span class="nn">MDAnalysis.topology.core</span> <span class="kn">import</span> <span class="n">build_segments</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;segid&quot;</span><span class="p">,</span> <span class="n">segid</span><span class="p">,</span> <span class="n">conversion</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+
+        <span class="c"># also updates convenience handles for segments in universe</span>
+        <span class="n">segments</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">_build_segments</span><span class="p">()</span>
+
+        <span class="c"># Note that this also automagically updates THIS AtomGroup;</span>
+        <span class="c"># the side effect of build_residues(self.atoms) is to update all Atoms!!!!</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_fill_cache</span><span class="p">(</span><span class="s">&#39;segments&#39;</span><span class="p">,</span> <span class="n">SegmentGroup</span><span class="p">(</span><span class="n">segments</span><span class="p">))</span>
+
+        <span class="c"># make sure to update the whole universe: the Atoms are shared but</span>
+        <span class="c"># ResidueGroups are not</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">_fill_cache</span><span class="p">(</span>
+                    <span class="s">&#39;segments&#39;</span><span class="p">,</span>
+                    <span class="n">SegmentGroup</span><span class="p">(</span><span class="n">segments</span><span class="p">))</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.set_mass"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_mass">[docs]</a>    <span class="k">def</span> <span class="nf">set_mass</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mass</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the atom mass to float *mass* for **all atoms** in the AtomGroup.</span>
+    <span class="n">set_segid</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_segids</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_segid&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_segids&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.set_masses"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_masses">[docs]</a>    <span class="k">def</span> <span class="nf">set_masses</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mass</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the atom masses to float *mass* for **all atoms** in the AtomGroup.</span>
+
+<span class="sd">        If *mass* is a sequence of the same length as the :class:`AtomGroup`</span>
+<span class="sd">        then each :attr:`Atom.mass` is set to the corresponding value. If</span>
+<span class="sd">        *value* is neither of length 1 (or a scalar) nor of the length of the</span>
+<span class="sd">        :class:`AtomGroup` then a :exc:`ValueError` is raised.</span>
 
 <span class="sd">        .. versionadded:: 0.7.4</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms and residues to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;mass&quot;</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span> <span class="n">conversion</span><span class="o">=</span><span class="nb">float</span><span class="p">,</span> <span class="n">cache</span><span class="o">=</span><span class="s">&quot;masses&quot;</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.set_type"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_type">[docs]</a>    <span class="k">def</span> <span class="nf">set_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atype</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the atom type to *atype* for **all atoms** in the AtomGroup.</span>
+    <span class="n">set_mass</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_masses</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_mass&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_masses&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.set_types"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_types">[docs]</a>    <span class="k">def</span> <span class="nf">set_types</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atype</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the atom types to *atype* for **all atoms** in the AtomGroup.</span>
+
+<span class="sd">        If *atype* is a sequence of the same length as the :class:`AtomGroup`</span>
+<span class="sd">        then each :attr:`Atom.atype` is set to the corresponding value. If</span>
+<span class="sd">        *value* is neither of length 1 (or a scalar) nor of the length of the</span>
+<span class="sd">        :class:`AtomGroup` then a :exc:`ValueError` is raised.</span>
 
 <span class="sd">        .. versionadded:: 0.7.4</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms and residues to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;type&quot;</span><span class="p">,</span> <span class="n">atype</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.set_charge"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_charge">[docs]</a>    <span class="k">def</span> <span class="nf">set_charge</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">charge</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the partial charge to float *charge* for **all atoms** in the AtomGroup.</span>
+    <span class="n">set_type</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_types</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_type&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_types&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.set_charges"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_charges">[docs]</a>    <span class="k">def</span> <span class="nf">set_charges</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">charge</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the partial charges to float *charge* for **all atoms** in the AtomGroup.</span>
+
+<span class="sd">        If *charge* is a sequence of the same length as the :class:`AtomGroup`</span>
+<span class="sd">        then each :attr:`Atom.charge` is set to the corresponding value. If</span>
+<span class="sd">        *value* is neither of length 1 (or a scalar) nor of the length of the</span>
+<span class="sd">        :class:`AtomGroup` then a :exc:`ValueError` is raised.</span>
 
 <span class="sd">        .. versionadded:: 0.7.4</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms and residues to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;charge&quot;</span><span class="p">,</span> <span class="n">charge</span><span class="p">,</span> <span class="n">conversion</span><span class="o">=</span><span class="nb">float</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.set_radius"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_radius">[docs]</a>    <span class="k">def</span> <span class="nf">set_radius</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">radius</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the atom radius to float *radius* for **all atoms** in the AtomGroup.</span>
+    <span class="n">set_charge</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_charges</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_charge&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_charges&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.set_radii"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_radii">[docs]</a>    <span class="k">def</span> <span class="nf">set_radii</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">radius</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the atom radii to float *radius* for **all atoms** in the AtomGroup.</span>
+
+<span class="sd">        If *radius* is a sequence of the same length as the :class:`AtomGroup`</span>
+<span class="sd">        then each :attr:`Atom.radius` is set to the corresponding value. If</span>
+<span class="sd">        *value* is neither of length 1 (or a scalar) nor of the length of the</span>
+<span class="sd">        :class:`AtomGroup` then a :exc:`ValueError` is raised.</span>
 
 <span class="sd">        .. versionadded:: 0.7.4</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms and residues to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;radius&quot;</span><span class="p">,</span> <span class="n">radius</span><span class="p">,</span> <span class="n">conversion</span><span class="o">=</span><span class="nb">float</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.set_bfactor"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_bfactor">[docs]</a>    <span class="k">def</span> <span class="nf">set_bfactor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">bfactor</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the atom bfactor to float *bfactor* for **all atoms** in the AtomGroup.</span>
+    <span class="n">set_radius</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_radii</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_radius&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_radii&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.set_bfactors"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_bfactors">[docs]</a>    <span class="k">def</span> <span class="nf">set_bfactors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">bfactor</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the atom bfactors to float *bfactor* for **all atoms** in the AtomGroup.</span>
+
+<span class="sd">        If *bfactor* is a sequence of the same length as the :class:`AtomGroup`</span>
+<span class="sd">        then each :attr:`Atom.bfactor` is set to the corresponding value. If</span>
+<span class="sd">        *value* is neither of length 1 (or a scalar) nor of the length of the</span>
+<span class="sd">        :class:`AtomGroup` then a :exc:`ValueError` is raised.</span>
 
 <span class="sd">        .. versionadded:: 0.7.4</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms and residues to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;bfactor&quot;</span><span class="p">,</span> <span class="n">bfactor</span><span class="p">,</span> <span class="n">conversion</span><span class="o">=</span><span class="nb">float</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.set_altLoc"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_altLoc">[docs]</a>    <span class="k">def</span> <span class="nf">set_altLoc</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">altLoc</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the altLoc of atoms in this group</span>
+    <span class="n">set_bfactor</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_bfactors</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_bfactor&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_bfactors&#39;</span><span class="p">)</span>
 
-<span class="sd">        This can apply a single value to all atoms, or a series of</span>
-<span class="sd">        values to each atom</span>
+<div class="viewcode-block" id="AtomGroup.set_altLocs"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_altLocs">[docs]</a>    <span class="k">def</span> <span class="nf">set_altLocs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">altLoc</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the altLocs to *altLoc for **all atoms** in the AtomGroup.</span>
+
+<span class="sd">        If *altLoc* is a sequence of the same length as the :class:`AtomGroup`</span>
+<span class="sd">        then each :attr:`Atom.altLoc` is set to the corresponding value. If</span>
+<span class="sd">        *value* is neither of length 1 (or a scalar) nor of the length of the</span>
+<span class="sd">        :class:`AtomGroup` then a :exc:`ValueError` is raised.</span>
 
 <span class="sd">        .. versionadded:: 0.11.0</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;altLoc&quot;</span><span class="p">,</span> <span class="n">altLoc</span><span class="p">,</span> <span class="n">conversion</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.set_serial"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_serial">[docs]</a>    <span class="k">def</span> <span class="nf">set_serial</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">serial</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the serial of atoms in this group</span>
+    <span class="n">set_altLoc</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_altLocs</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_altLoc&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_altLocs&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.set_serials"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_serials">[docs]</a>    <span class="k">def</span> <span class="nf">set_serials</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">serial</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the serials to *serial* for **all atoms** in the AtomGroup.</span>
 
-<span class="sd">        This can apply a single value to all atoms, or a series of</span>
-<span class="sd">        values to each atom</span>
+<span class="sd">        If *serial* is a sequence of the same length as the :class:`AtomGroup`</span>
+<span class="sd">        then each :attr:`Atom.serial` is set to the corresponding value. If</span>
+<span class="sd">        *value* is neither of length 1 (or a scalar) nor of the length of the</span>
+<span class="sd">        :class:`AtomGroup` then a :exc:`ValueError` is raised.</span>
 
 <span class="sd">        .. versionadded:: 0.11.0</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;serial&quot;</span><span class="p">,</span> <span class="n">serial</span><span class="p">,</span> <span class="n">conversion</span><span class="o">=</span><span class="nb">int</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.centerOfGeometry"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry">[docs]</a>    <span class="k">def</span> <span class="nf">centerOfGeometry</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+    <span class="n">set_serial</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_serials</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_serial&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_serials&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.center_of_geometry"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry">[docs]</a>    <span class="k">def</span> <span class="nf">center_of_geometry</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Center of geometry (also known as centroid) of the selection.</span>
 
 <span class="sd">        :Keywords:</span>
@@ -1895,13 +1971,16 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">pbc</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;pbc&#39;</span><span class="p">,</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;use_pbc&#39;</span><span class="p">])</span>
         <span class="k">if</span> <span class="n">pbc</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">packIntoBox</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span>
+            <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pack_into_box</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">positions</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span>
 </div>
-    <span class="n">centroid</span> <span class="o">=</span> <span class="n">centerOfGeometry</span>
+    <span class="n">centerOfGeometry</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">center_of_geometry</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;centerOfGeometry&#39;</span><span class="p">,</span>
+                                 <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;center_of_geometry&#39;</span><span class="p">)</span>
+
+    <span class="n">centroid</span> <span class="o">=</span> <span class="n">center_of_geometry</span>
 
-<div class="viewcode-block" id="AtomGroup.centerOfMass"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass">[docs]</a>    <span class="k">def</span> <span class="nf">centerOfMass</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="AtomGroup.center_of_mass"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.center_of_mass">[docs]</a>    <span class="k">def</span> <span class="nf">center_of_mass</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Center of mass of the selection.</span>
 
 <span class="sd">        :Keywords:</span>
@@ -1916,12 +1995,14 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">pbc</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;pbc&#39;</span><span class="p">,</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;use_pbc&#39;</span><span class="p">])</span>
         <span class="k">if</span> <span class="n">pbc</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">packIntoBox</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">masses</span><span class="p">[:,</span> <span class="n">numpy</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span>
-                             <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">totalMass</span><span class="p">()</span>
+            <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pack_into_box</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">masses</span><span class="p">[:,</span> <span class="n">numpy</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span>
+                             <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">total_mass</span><span class="p">()</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">positions</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">masses</span><span class="p">[:,</span> <span class="n">numpy</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">totalMass</span><span class="p">()</span>
+            <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">positions</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">masses</span><span class="p">[:,</span> <span class="n">numpy</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">total_mass</span><span class="p">()</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.radiusOfGyration"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.radiusOfGyration">[docs]</a>    <span class="k">def</span> <span class="nf">radiusOfGyration</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+    <span class="n">centerOfMass</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">center_of_mass</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;centerOfMass&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;center_of_mass&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.radius_of_gyration"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.radius_of_gyration">[docs]</a>    <span class="k">def</span> <span class="nf">radius_of_gyration</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Radius of gyration.</span>
 
 <span class="sd">        :Keywords:</span>
@@ -1937,13 +2018,15 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="n">pbc</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;pbc&#39;</span><span class="p">,</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;use_pbc&#39;</span><span class="p">])</span>
         <span class="n">masses</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">masses</span>
         <span class="k">if</span> <span class="n">pbc</span><span class="p">:</span>
-            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">packIntoBox</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pack_into_box</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">positions</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
-        <span class="n">rog_sq</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">masses</span> <span class="o">*</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">recenteredpos</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">))</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">totalMass</span><span class="p">()</span>
+            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">positions</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
+        <span class="n">rog_sq</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">masses</span> <span class="o">*</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">recenteredpos</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">))</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">total_mass</span><span class="p">()</span>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">rog_sq</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.shapeParameter"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.shapeParameter">[docs]</a>    <span class="k">def</span> <span class="nf">shapeParameter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+    <span class="n">radiusOfGyration</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">radius_of_gyration</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;radiusOfGyration&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;radius_of_gyration&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.shape_parameter"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.shape_parameter">[docs]</a>    <span class="k">def</span> <span class="nf">shape_parameter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Shape parameter.</span>
 
 <span class="sd">        See [Dima2004]_ for background information.</span>
@@ -1962,18 +2045,20 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="n">pbc</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;pbc&#39;</span><span class="p">,</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;use_pbc&#39;</span><span class="p">])</span>
         <span class="n">masses</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">masses</span>
         <span class="k">if</span> <span class="n">pbc</span><span class="p">:</span>
-            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">packIntoBox</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pack_into_box</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">positions</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
+            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">positions</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
         <span class="n">tensor</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
         <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">xrange</span><span class="p">(</span><span class="n">recenteredpos</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
             <span class="n">tensor</span> <span class="o">+=</span> <span class="n">masses</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> <span class="o">*</span> <span class="n">numpy</span><span class="o">.</span><span class="n">outer</span><span class="p">(</span><span class="n">recenteredpos</span><span class="p">[</span><span class="n">x</span><span class="p">,</span> <span class="p">:],</span>
                                               <span class="n">recenteredpos</span><span class="p">[</span><span class="n">x</span><span class="p">,</span> <span class="p">:])</span>
-        <span class="n">tensor</span> <span class="o">/=</span> <span class="bp">self</span><span class="o">.</span><span class="n">totalMass</span><span class="p">()</span>
+        <span class="n">tensor</span> <span class="o">/=</span> <span class="bp">self</span><span class="o">.</span><span class="n">total_mass</span><span class="p">()</span>
         <span class="n">eig_vals</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eigvalsh</span><span class="p">(</span><span class="n">tensor</span><span class="p">)</span>
         <span class="n">shape</span> <span class="o">=</span> <span class="mf">27.0</span> <span class="o">*</span> <span class="n">numpy</span><span class="o">.</span><span class="n">prod</span><span class="p">(</span><span class="n">eig_vals</span> <span class="o">-</span> <span class="n">numpy</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">eig_vals</span><span class="p">))</span> <span class="o">/</span> <span class="n">numpy</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">eig_vals</span><span class="p">),</span> <span class="mi">3</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">shape</span>
 </div>
+    <span class="n">shapeParameter</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">shape_parameter</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;shapeParameter&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;shape_parameter&#39;</span><span class="p">)</span>
+
 <div class="viewcode-block" id="AtomGroup.asphericity"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.asphericity">[docs]</a>    <span class="k">def</span> <span class="nf">asphericity</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Asphericity.</span>
 
@@ -1993,20 +2078,20 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="n">pbc</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;pbc&#39;</span><span class="p">,</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;use_pbc&#39;</span><span class="p">])</span>
         <span class="n">masses</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">masses</span>
         <span class="k">if</span> <span class="n">pbc</span><span class="p">:</span>
-            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">packIntoBox</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pack_into_box</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">positions</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
+            <span class="n">recenteredpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">positions</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
         <span class="n">tensor</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
         <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">xrange</span><span class="p">(</span><span class="n">recenteredpos</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
             <span class="n">tensor</span> <span class="o">+=</span> <span class="n">masses</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> <span class="o">*</span> <span class="n">numpy</span><span class="o">.</span><span class="n">outer</span><span class="p">(</span><span class="n">recenteredpos</span><span class="p">[</span><span class="n">x</span><span class="p">,</span> <span class="p">:],</span>
                                               <span class="n">recenteredpos</span><span class="p">[</span><span class="n">x</span><span class="p">,</span> <span class="p">:])</span>
-        <span class="n">tensor</span> <span class="o">/=</span> <span class="bp">self</span><span class="o">.</span><span class="n">totalMass</span><span class="p">()</span>
+        <span class="n">tensor</span> <span class="o">/=</span> <span class="bp">self</span><span class="o">.</span><span class="n">total_mass</span><span class="p">()</span>
         <span class="n">eig_vals</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eigvalsh</span><span class="p">(</span><span class="n">tensor</span><span class="p">)</span>
         <span class="n">shape</span> <span class="o">=</span> <span class="p">(</span><span class="mf">3.0</span> <span class="o">/</span> <span class="mf">2.0</span><span class="p">)</span> <span class="o">*</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">eig_vals</span> <span class="o">-</span> <span class="n">numpy</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">eig_vals</span><span class="p">),</span> <span class="mi">2</span><span class="p">))</span> <span class="o">/</span> <span class="n">numpy</span><span class="o">.</span><span class="n">power</span><span class="p">(</span>
             <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">eig_vals</span><span class="p">),</span> <span class="mi">2</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">shape</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.momentOfInertia"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.momentOfInertia">[docs]</a>    <span class="k">def</span> <span class="nf">momentOfInertia</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="AtomGroup.moment_of_inertia"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.moment_of_inertia">[docs]</a>    <span class="k">def</span> <span class="nf">moment_of_inertia</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Tensor of inertia as 3x3 NumPy array.</span>
 
 <span class="sd">        :Keywords:</span>
@@ -2022,9 +2107,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="n">pbc</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;pbc&#39;</span><span class="p">,</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;use_pbc&#39;</span><span class="p">])</span>
         <span class="c"># Convert to local coordinates</span>
         <span class="k">if</span> <span class="n">pbc</span><span class="p">:</span>
-            <span class="n">pos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">packIntoBox</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+            <span class="n">pos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pack_into_box</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="n">pos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">positions</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
+            <span class="n">pos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">positions</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
 
         <span class="n">masses</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">masses</span>
         <span class="c"># Create the inertia tensor</span>
@@ -2052,6 +2137,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 
         <span class="k">return</span> <span class="n">tens</span>
 </div>
+    <span class="n">momentOfInertia</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">moment_of_inertia</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;momentOfInertia&#39;</span><span class="p">,</span>
+                                <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;moment_of_inertia&#39;</span><span class="p">)</span>
+
 <div class="viewcode-block" id="AtomGroup.bbox"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.bbox">[docs]</a>    <span class="k">def</span> <span class="nf">bbox</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Return the bounding box of the selection.</span>
 
@@ -2075,7 +2163,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">pbc</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;pbc&#39;</span><span class="p">,</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;use_pbc&#39;</span><span class="p">])</span>
         <span class="k">if</span> <span class="n">pbc</span><span class="p">:</span>
-            <span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">packIntoBox</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
+            <span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pack_into_box</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">x</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">),</span> <span class="n">x</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)])</span>
@@ -2100,16 +2188,16 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">pbc</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;pbc&#39;</span><span class="p">,</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;use_pbc&#39;</span><span class="p">])</span>
         <span class="k">if</span> <span class="n">pbc</span><span class="p">:</span>
-            <span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">packIntoBox</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
-            <span class="n">centroid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+            <span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pack_into_box</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
+            <span class="n">centroid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span>
-            <span class="n">centroid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
+            <span class="n">centroid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
         <span class="n">R</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">square</span><span class="p">(</span><span class="n">x</span> <span class="o">-</span> <span class="n">centroid</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)))</span>
         <span class="k">return</span> <span class="n">R</span><span class="p">,</span> <span class="n">centroid</span>
 </div>
     <span class="nd">@property</span>
-<div class="viewcode-block" id="AtomGroup.bond"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.bond">[docs]</a>    <span class="k">def</span> <span class="nf">bond</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">bond</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;This AtomGroup represented as a Bond object</span>
 
 <span class="sd">        :Returns:</span>
@@ -2123,9 +2211,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">2</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">&quot;bond only makes sense for a group with exactly 2 atoms&quot;</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">Bond</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="AtomGroup.angle"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.angle">[docs]</a>    <span class="k">def</span> <span class="nf">angle</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">angle</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;This AtomGroup represented as an Angle object</span>
 
 <span class="sd">        :Returns:</span>
@@ -2139,9 +2227,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">3</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">&quot;angle only makes sense for a group with exactly 3 atoms&quot;</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">Angle</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="AtomGroup.dihedral"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.dihedral">[docs]</a>    <span class="k">def</span> <span class="nf">dihedral</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dihedral</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;This AtomGroup represented as a Dihedral object</span>
 
 <span class="sd">        :Returns:</span>
@@ -2156,9 +2244,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">&quot;dihedral only makes sense for a group with exactly 4 atoms&quot;</span><span class="p">)</span>
 
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">Dihedral</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="AtomGroup.improper"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.improper">[docs]</a>    <span class="k">def</span> <span class="nf">improper</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">improper</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;This AtomGroup represented as an ImproperDihedral object</span>
 
 <span class="sd">        :Returns:</span>
@@ -2173,11 +2261,11 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">&quot;improper only makes sense for a group with exactly 4 atoms&quot;</span><span class="p">)</span>
 
         <span class="k">return</span> <span class="n">top</span><span class="o">.</span><span class="n">ImproperDihedral</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
-</div>
-<div class="viewcode-block" id="AtomGroup.principalAxes"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.principalAxes">[docs]</a>    <span class="k">def</span> <span class="nf">principalAxes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+<div class="viewcode-block" id="AtomGroup.principal_axes"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.principal_axes">[docs]</a>    <span class="k">def</span> <span class="nf">principal_axes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Calculate the principal axes from the moment of inertia.</span>
 
-<span class="sd">        e1,e2,e3 = AtomGroup.principalAxes()</span>
+<span class="sd">        e1,e2,e3 = AtomGroup.principal_axes()</span>
 
 <span class="sd">        The eigenvectors are sorted by eigenvalue, i.e. the first one</span>
 <span class="sd">        corresponds to the highest eigenvalue and is thus the first principal axes.</span>
@@ -2197,14 +2285,16 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">pbc</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;pbc&#39;</span><span class="p">,</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;use_pbc&#39;</span><span class="p">])</span>
         <span class="k">if</span> <span class="n">pbc</span><span class="p">:</span>
-            <span class="n">eigenval</span><span class="p">,</span> <span class="n">eigenvec</span> <span class="o">=</span> <span class="n">eig</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">momentOfInertia</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">))</span>
+            <span class="n">eigenval</span><span class="p">,</span> <span class="n">eigenvec</span> <span class="o">=</span> <span class="n">eig</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">moment_of_inertia</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">True</span><span class="p">))</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="n">eigenval</span><span class="p">,</span> <span class="n">eigenvec</span> <span class="o">=</span> <span class="n">eig</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">momentOfInertia</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">))</span>
+            <span class="n">eigenval</span><span class="p">,</span> <span class="n">eigenvec</span> <span class="o">=</span> <span class="n">eig</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">moment_of_inertia</span><span class="p">(</span><span class="n">pbc</span><span class="o">=</span><span class="bp">False</span><span class="p">))</span>
         <span class="c"># Sort</span>
         <span class="n">indices</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">argsort</span><span class="p">(</span><span class="n">eigenval</span><span class="p">)</span>
         <span class="c"># Return transposed in more logical form. See Issue 33.</span>
         <span class="k">return</span> <span class="n">eigenvec</span><span class="p">[:,</span> <span class="n">indices</span><span class="p">]</span><span class="o">.</span><span class="n">T</span>
 </div>
+    <span class="n">principalAxes</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">principal_axes</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;principalAxes&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;principal_axes&#39;</span><span class="p">)</span>
+
 <div class="viewcode-block" id="AtomGroup.get_positions"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.get_positions">[docs]</a>    <span class="k">def</span> <span class="nf">get_positions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ts</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">copy</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">numpy</span><span class="o">.</span><span class="n">float32</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Get a NumPy array of the coordinates.</span>
 
@@ -2558,13 +2648,13 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">M</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">M</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.align_principalAxis"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.align_principalAxis">[docs]</a>    <span class="k">def</span> <span class="nf">align_principalAxis</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">axis</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
+<div class="viewcode-block" id="AtomGroup.align_principal_axis"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.align_principal_axis">[docs]</a>    <span class="k">def</span> <span class="nf">align_principal_axis</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">axis</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Align principal axis with index *axis* with *vector*.</span>
 
 <span class="sd">        :Arguments:</span>
 <span class="sd">          *axis*</span>
 <span class="sd">            Index of the principal axis (0, 1, or 2), as produced by</span>
-<span class="sd">            :meth:`~MDAnalysis.core.AtomGroup.AtomGroup.principalAxes`.</span>
+<span class="sd">            :meth:`~MDAnalysis.core.AtomGroup.AtomGroup.principal_axes`.</span>
 <span class="sd">          *vector*</span>
 <span class="sd">            A 3D vector such as the z-axis (``[0,0,1]``); can be</span>
 <span class="sd">            anything that looks like a list with three entries.</span>
@@ -2572,17 +2662,21 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">        To align the long axis of a channel (the first principal axis,</span>
 <span class="sd">        i.e. *axis* = 0) with the z-axis::</span>
 
-<span class="sd">          u.atoms.align_principalAxis(0, [0,0,1])</span>
+<span class="sd">          u.atoms.align_principal_axis(0, [0,0,1])</span>
 <span class="sd">          u.atoms.write(&quot;aligned.pdb&quot;)</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">p</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">principalAxes</span><span class="p">()[</span><span class="n">axis</span><span class="p">]</span>
+        <span class="n">p</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">principal_axes</span><span class="p">()[</span><span class="n">axis</span><span class="p">]</span>
         <span class="n">angle</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">degrees</span><span class="p">(</span><span class="n">mdamath</span><span class="o">.</span><span class="n">angle</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">vector</span><span class="p">))</span>
         <span class="n">ax</span> <span class="o">=</span> <span class="n">transformations</span><span class="o">.</span><span class="n">rotaxis</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">vector</span><span class="p">)</span>
         <span class="c">#print &quot;principal[%d] = %r&quot; % (axis, p)</span>
         <span class="c">#print &quot;axis = %r, angle = %f deg&quot; % (ax, angle)</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">rotateby</span><span class="p">(</span><span class="n">angle</span><span class="p">,</span> <span class="n">ax</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="AtomGroup.packIntoBox"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.packIntoBox">[docs]</a>    <span class="k">def</span> <span class="nf">packIntoBox</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
+    <span class="n">align_principalAxis</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">align_principal_axis</span><span class="p">,</span>
+                                    <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;align_principalAxis&#39;</span><span class="p">,</span>
+                                    <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;align_principal_axis&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtomGroup.pack_into_box"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.pack_into_box">[docs]</a>    <span class="k">def</span> <span class="nf">pack_into_box</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
         <span class="sd">r&quot;&quot;&quot;Shift all atoms in this group to be within the primary unit cell.</span>
 
 <span class="sd">        AtomGroup.packintobox([box, [inplace=True]])</span>
@@ -2630,16 +2724,18 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 
         <span class="n">coords</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">positions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">]</span>
         <span class="k">if</span> <span class="ow">not</span> <span class="n">inplace</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">distances</span><span class="o">.</span><span class="n">applyPBC</span><span class="p">(</span><span class="n">coords</span><span class="p">,</span> <span class="n">box</span><span class="p">)</span>
+            <span class="k">return</span> <span class="n">distances</span><span class="o">.</span><span class="n">apply_PBC</span><span class="p">(</span><span class="n">coords</span><span class="p">,</span> <span class="n">box</span><span class="p">)</span>
 
-        <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">positions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">]</span> <span class="o">=</span> <span class="n">distances</span><span class="o">.</span><span class="n">applyPBC</span><span class="p">(</span><span class="n">coords</span><span class="p">,</span> <span class="n">box</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">positions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">]</span> <span class="o">=</span> <span class="n">distances</span><span class="o">.</span><span class="n">apply_PBC</span><span class="p">(</span><span class="n">coords</span><span class="p">,</span> <span class="n">box</span><span class="p">)</span>
 
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">positions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">]</span>
 </div>
+    <span class="n">packIntoBox</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">pack_into_box</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;packIntoBox&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;pack_into_box&#39;</span><span class="p">)</span>
+
 <div class="viewcode-block" id="AtomGroup.wrap"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.wrap">[docs]</a>    <span class="k">def</span> <span class="nf">wrap</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">compound</span><span class="o">=</span><span class="s">&quot;atoms&quot;</span><span class="p">,</span> <span class="n">center</span><span class="o">=</span><span class="s">&quot;com&quot;</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Shift the contents of this AtomGroup back into the unit cell.</span>
 
-<span class="sd">        This is a more powerful version of :meth:`packIntoBox`, allowing</span>
+<span class="sd">        This is a more powerful version of :meth:`pack_into_box`, allowing</span>
 <span class="sd">        groups of atoms to be kept together through the process.</span>
 
 <span class="sd">        :Keywords:</span>
@@ -2678,12 +2774,12 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">        will be used.</span>
 
 <span class="sd">        .. Note::</span>
-<span class="sd">           wrap with all default keywords is identical to :meth:`packIntoBox`</span>
+<span class="sd">           wrap with all default keywords is identical to :meth:`pack_into_box`</span>
 
 <span class="sd">        .. versionadded:: 0.9.2</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="n">compound</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">&quot;atoms&quot;</span><span class="p">:</span>
-            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">packIntoBox</span><span class="p">(</span><span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">)</span>
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">pack_into_box</span><span class="p">(</span><span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">)</span>
 
         <span class="k">if</span> <span class="n">compound</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">&#39;group&#39;</span><span class="p">:</span>
             <span class="n">objects</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">]</span>
@@ -2699,9 +2795,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
                              <span class="s">&quot;or &#39;fragments&#39;&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">compound</span><span class="p">))</span>
 
         <span class="k">if</span> <span class="n">center</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&#39;com&#39;</span><span class="p">,</span> <span class="s">&#39;centerofmass&#39;</span><span class="p">):</span>
-            <span class="n">centers</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">vstack</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">objects</span><span class="p">])</span>
+            <span class="n">centers</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">vstack</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">objects</span><span class="p">])</span>
         <span class="k">elif</span> <span class="n">center</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&#39;cog&#39;</span><span class="p">,</span> <span class="s">&#39;centroid&#39;</span><span class="p">,</span> <span class="s">&#39;centerofgeometry&#39;</span><span class="p">):</span>
-            <span class="n">centers</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">vstack</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">objects</span><span class="p">])</span>
+            <span class="n">centers</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">vstack</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">objects</span><span class="p">])</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">&quot;Unrecognised center definition: {0}&quot;</span>
                              <span class="s">&quot;Please use one of &#39;com&#39; or &#39;cog&#39;&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">center</span><span class="p">))</span>
@@ -2711,7 +2807,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
             <span class="n">box</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">dimensions</span>
 
         <span class="c"># calculate shift per object center</span>
-        <span class="n">dests</span> <span class="o">=</span> <span class="n">distances</span><span class="o">.</span><span class="n">applyPBC</span><span class="p">(</span><span class="n">centers</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">)</span>
+        <span class="n">dests</span> <span class="o">=</span> <span class="n">distances</span><span class="o">.</span><span class="n">apply_PBC</span><span class="p">(</span><span class="n">centers</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">)</span>
         <span class="n">shifts</span> <span class="o">=</span> <span class="n">dests</span> <span class="o">-</span> <span class="n">centers</span>
 
         <span class="k">for</span> <span class="n">o</span><span class="p">,</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">izip</span><span class="p">(</span><span class="n">objects</span><span class="p">,</span> <span class="n">shifts</span><span class="p">):</span>
@@ -2747,7 +2843,6 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="sd">&quot;&quot;&quot;Split atomgroup into a list of atomgroups by *level*.</span>
 
 <span class="sd">        *level* can be &quot;atom&quot;, &quot;residue&quot;, &quot;segment&quot;.</span>
-
 <span class="sd">        .. versionadded:: 0.9.0</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="c"># CHECK: What happens to duplicate atoms (with advanced slicing)?</span>
@@ -2900,15 +2995,15 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s">&quot;This AtomGroup does not belong to a Universe with a dimension.&quot;</span><span class="p">)</span>
 
     <span class="nd">@dimensions.setter</span>
-<div class="viewcode-block" id="AtomGroup.dimensions"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.dimensions">[docs]</a>    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Pass on to Universe setter</span>
 
 <span class="sd">        .. versionadded:: 0.9.0</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">dimensions</span> <span class="o">=</span> <span class="n">box</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="AtomGroup.ts"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.ts">[docs]</a>    <span class="k">def</span> <span class="nf">ts</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">ts</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Temporary Timestep that contains the selection coordinates.</span>
 
 <span class="sd">        A :class:`~MDAnalysis.coordinates.base.Timestep` instance,</span>
@@ -2930,7 +3025,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">_ts</span> <span class="o">=</span> <span class="n">trj_ts</span><span class="o">.</span><span class="n">copy_slice</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">)</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ts</span>
 
-</div></div>
+</div>
 <div class="viewcode-block" id="Residue"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Residue">[docs]</a><span class="k">class</span> <span class="nc">Residue</span><span class="p">(</span><span class="n">AtomGroup</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;A group of atoms corresponding to a residue.</span>
 
@@ -3120,8 +3215,58 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 
     <span class="nb">set</span> <span class="o">=</span> <span class="n">_set_residues</span>
 
-<div class="viewcode-block" id="ResidueGroup.set_resid"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.set_resid">[docs]</a>    <span class="k">def</span> <span class="nf">set_resid</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resid</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the resid to integer *resid* for **all residues** in the :class:`ResidueGroup`.</span>
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">resids</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Returns an array of residue numbers.</span>
+
+<span class="sd">        .. versionchanged:: 0.8</span>
+<span class="sd">           Returns a :class:`numpy.ndarray`</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Now a property and returns array of length `len(self)`</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">id</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">resnames</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Returns an array of residue names.</span>
+
+<span class="sd">        .. versionchanged:: 0.8</span>
+<span class="sd">           Returns a :class:`numpy.ndarray`</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Now a property and returns array of length `len(self)`</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">resnums</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Returns an array of canonical residue numbers.</span>
+
+<span class="sd">        .. versionadded:: 0.7.4</span>
+<span class="sd">        .. versionchanged:: 0.8</span>
+<span class="sd">           Returns a :class:`numpy.ndarray`</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Now a property and returns array of length `len(self)`</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">resnum</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">segids</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Returns an array of segment names.</span>
+
+<span class="sd">        .. note:: uses the segment of the first atom in each residue for the</span>
+<span class="sd">                  segment name returned</span>
+
+<span class="sd">        .. versionchanged:: 0.8</span>
+<span class="sd">           Returns a :class:`numpy.ndarray`</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Now a property and returns array of length `len(self)`</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c"># a bit of a hack to use just</span>
+        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">segid</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+
+<div class="viewcode-block" id="ResidueGroup.set_resids"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.set_resids">[docs]</a>    <span class="k">def</span> <span class="nf">set_resids</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resid</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the resids to integer *resid* for **all residues** in the</span>
+<span class="sd">        :class:`ResidueGroup`.</span>
 
 <span class="sd">        If *resid* is a sequence of the same length as the :class:`ResidueGroup`</span>
 <span class="sd">        then each :attr:`Atom.resid` is set to the corresponding value together</span>
@@ -3145,19 +3290,15 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">           everything else is derived from these atoms.</span>
 
 <span class="sd">        .. versionadded:: 0.8</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="kn">from</span> <span class="nn">MDAnalysis.topology.core</span> <span class="kn">import</span> <span class="n">build_residues</span>
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&#39;resid&#39;</span><span class="p">,</span> <span class="n">resid</span><span class="p">)</span>
-        <span class="n">residues</span> <span class="o">=</span> <span class="n">build_residues</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
-        <span class="c"># update THIS residue group</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="o">.</span><span class="n">_residues</span> <span class="o">=</span> <span class="n">residues</span>
-        <span class="c"># make sure to update the whole universe: the Atoms are shared but ResidueGroups are not</span>
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">_fill_cache</span><span class="p">(</span><span class="s">&#39;residues&#39;</span><span class="p">,</span> <span class="n">build_residues</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="p">))</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">ResidueGroup</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">set_resids</span><span class="p">(</span><span class="n">resid</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="ResidueGroup.set_resnum"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.set_resnum">[docs]</a>    <span class="k">def</span> <span class="nf">set_resnum</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resnum</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the resnum to *resnum* for **all residues** in the :class:`ResidueGroup`.</span>
+    <span class="n">set_resid</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_resids</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_resid&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_resids&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="ResidueGroup.set_resnums"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.set_resnums">[docs]</a>    <span class="k">def</span> <span class="nf">set_resnums</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resnum</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the resnums to *resnum* for **all residues** in the :class:`ResidueGroup`.</span>
 
 <span class="sd">        If *resnum* is a sequence of the same length as the :class:`ResidueGroup`</span>
 <span class="sd">        then each :attr:`Atom.resnum` is set to the corresponding value together</span>
@@ -3177,11 +3318,16 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">           Also changes the residues.</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms and residues to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;resnum&quot;</span><span class="p">,</span> <span class="n">resnum</span><span class="p">)</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">ResidueGroup</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">set_resnums</span><span class="p">(</span><span class="n">resnum</span><span class="p">)</span>
 </div>
-<div class="viewcode-block" id="ResidueGroup.set_resname"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.set_resname">[docs]</a>    <span class="k">def</span> <span class="nf">set_resname</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resname</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the resname to string *resname* for **all residues** in the :class:`ResidueGroup`.</span>
+    <span class="n">set_resnum</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_resnums</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_resnum&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_resnums&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="ResidueGroup.set_resnames"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.set_resnames">[docs]</a>    <span class="k">def</span> <span class="nf">set_resnames</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resname</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the resnames to string *resname* for **all residues** in the</span>
+<span class="sd">        :class:`ResidueGroup`.</span>
 
 <span class="sd">        If *resname* is a sequence of the same length as the :class:`ResidueGroup`</span>
 <span class="sd">        then each :attr:`Atom.resname` is set to the corresponding value together</span>
@@ -3194,17 +3340,21 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">           Also changes the residues.</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms and residues to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&quot;resname&quot;</span><span class="p">,</span> <span class="n">resname</span><span class="p">,</span> <span class="n">conversion</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">ResidueGroup</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">set_resnames</span><span class="p">(</span><span class="n">resname</span><span class="p">)</span>
+</div>
+    <span class="n">set_resname</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_resnames</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_resname&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_resnames&#39;</span><span class="p">)</span>
 
     <span class="c"># All other AtomGroup.set_xxx() methods should just work as</span>
     <span class="c"># ResidueGroup.set_xxx() because we overrode self.set(); the ones above</span>
     <span class="c"># where kept separate because we can save a call to build_residues()</span>
     <span class="c"># because there is no ambiguity as which residues are changed.</span>
-</div>
+
     <span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">return</span> <span class="s">&quot;&lt;ResidueGroup {res}&gt;&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
-            <span class="n">res</span><span class="o">=</span><span class="nb">repr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_residues</span><span class="p">))</span>
+            <span class="n">res</span><span class="o">=</span><span class="nb">repr</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">)))</span>
 
 </div>
 <div class="viewcode-block" id="Segment"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Segment">[docs]</a><span class="k">class</span> <span class="nc">Segment</span><span class="p">(</span><span class="n">ResidueGroup</span><span class="p">):</span>
@@ -3239,7 +3389,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="sd">&quot;&quot;&quot;Initialize a Segment with segid *name* from a list of :class:`Residue` instances.&quot;&quot;&quot;</span>
         <span class="nb">super</span><span class="p">(</span><span class="n">Segment</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="n">residues</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
-        <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_residues</span><span class="p">:</span>
+        <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
             <span class="n">res</span><span class="o">.</span><span class="n">segment</span> <span class="o">=</span> <span class="bp">self</span>
             <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">res</span><span class="p">:</span>
                 <span class="n">atom</span><span class="o">.</span><span class="n">segment</span> <span class="o">=</span> <span class="bp">self</span>
@@ -3251,9 +3401,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span>
 
     <span class="nd">@id.setter</span>
-<div class="viewcode-block" id="Segment.id"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Segment.id">[docs]</a>    <span class="k">def</span> <span class="nf">id</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">id</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">x</span>
-</div>
+
     <span class="k">def</span> <span class="nf">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
         <span class="k">if</span> <span class="n">attr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;r&#39;</span><span class="p">:</span>
             <span class="n">resnum</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">attr</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span> <span class="o">-</span> <span class="mi">1</span>  <span class="c"># 1-based for the user, 0-based internally</span>
@@ -3261,7 +3411,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">else</span><span class="p">:</span>
             <span class="c"># There can be multiple residues with the same name</span>
             <span class="n">r</span> <span class="o">=</span> <span class="p">[]</span>
-            <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_residues</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
                 <span class="k">if</span> <span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">attr</span><span class="p">):</span>
                     <span class="n">r</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">res</span><span class="p">)</span>
             <span class="k">if</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">r</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">):</span>
@@ -3329,8 +3479,19 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 
     <span class="nb">set</span> <span class="o">=</span> <span class="n">_set_segments</span>
 
-<div class="viewcode-block" id="SegmentGroup.set_segid"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.SegmentGroup.set_segid">[docs]</a>    <span class="k">def</span> <span class="nf">set_segid</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">segid</span><span class="p">,</span> <span class="n">buildsegments</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Set the segid to *segid* for all atoms in the :class:`SegmentGroup`.</span>
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">segids</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Returns an array of segment names.</span>
+
+<span class="sd">        .. versionchanged:: 0.8</span>
+<span class="sd">           Returns a :class:`numpy.ndarray`</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Now a property and returns array of length `len(self)`</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">s</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">segments</span><span class="p">])</span>
+
+<div class="viewcode-block" id="SegmentGroup.set_segids"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.SegmentGroup.set_segids">[docs]</a>    <span class="k">def</span> <span class="nf">set_segids</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">segid</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Set the segids to *segid* for all atoms in the :class:`SegmentGroup`.</span>
 
 <span class="sd">        If *segid* is a sequence of the same length as the :class:`SegmentGroup`</span>
 <span class="sd">        then each :attr:`Atom.segid` is set to the corresponding value together</span>
@@ -3342,47 +3503,24 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 
 <span class="sd">           :meth:`set_segid` can change the topology.</span>
 
-<span class="sd">           With the default *buildsegments* = ``True`` it can be used to join</span>
-<span class="sd">           segments or to break groups into multiple disjoint segments. Note</span>
-<span class="sd">           that each :class:`Atom` can only belong to a single</span>
-<span class="sd">           :class:`Segment`.</span>
-
-<span class="sd">        For performance reasons, *buildsegments* can be set to ``False``. Then</span>
-<span class="sd">        one needs to run :meth:`Universe._build_segments` manually later in</span>
-<span class="sd">        order to update the list of :class:`Segment` instances and regenerate</span>
-<span class="sd">        the segid instant selectors.</span>
-
-<span class="sd">        .. Warning::</span>
-
-<span class="sd">           The values of *this* :class:`SegmentGroup` are not being changed</span>
-<span class="sd">           (i.e. if you assign multiple segids this instance will not be broken</span>
-<span class="sd">           in multiple segments, rather you will have one :class:`SegmentGroup`</span>
-<span class="sd">           that groups multiple segments together). You **must create a new**</span>
-<span class="sd">           :class:`SegmentGroup` **from the** :class:`Universe` --- only</span>
-<span class="sd">           :class:`Atom` instances are changed, everything else is derived from</span>
-<span class="sd">           these atoms.</span>
-
+<span class="sd">           This can be used to join segments or to break groups into multiple</span>
+<span class="sd">           disjoint segments. Note that each :class:`Atom` can only belong to a</span>
+<span class="sd">           single :class:`Segment`.</span>
 
 <span class="sd">        .. versionadded:: 0.7.4</span>
 <span class="sd">        .. versionchanged:: 0.8</span>
 <span class="sd">           Can set atoms and residues to distinct values by providing a sequence or iterable.</span>
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Made plural to make consistent with corresponding property</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="nb">super</span><span class="p">(</span><span class="n">SegmentGroup</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">set_segid</span><span class="p">(</span><span class="n">segid</span><span class="p">,</span> <span class="n">buildsegments</span><span class="o">=</span><span class="n">buildsegments</span><span class="p">)</span>
-
-        <span class="c"># Is the following needed? -- orbeckst</span>
-        <span class="c"># also fix self --- otherwise users will get confused if the changes are not reflected in the</span>
-        <span class="c"># object they are currently using (it works automatically for AtomGroup but not higher order groups)</span>
-        <span class="c">#</span>
-        <span class="c"># This is a hack to be able to set properties on Segment/Atom</span>
-        <span class="c"># instances where they have different names</span>
-        <span class="c">#attr = {&#39;segid&#39;: &#39;id&#39;}</span>
-        <span class="k">for</span> <span class="n">seg</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">izip</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">segments</span><span class="p">,</span> <span class="n">itertools</span><span class="o">.</span><span class="n">cycle</span><span class="p">(</span><span class="n">util</span><span class="o">.</span><span class="n">asiterable</span><span class="p">(</span><span class="n">segid</span><span class="p">))):</span>
-            <span class="nb">setattr</span><span class="p">(</span><span class="n">seg</span><span class="p">,</span> <span class="s">&#39;name&#39;</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">SegmentGroup</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">set_segids</span><span class="p">(</span><span class="n">segid</span><span class="p">)</span>
 </div>
+    <span class="n">set_segid</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">set_segids</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;set_segid&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;set_segids&#39;</span><span class="p">)</span>
+
     <span class="k">def</span> <span class="nf">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
         <span class="k">if</span> <span class="n">attr</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">&#39;s&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="n">attr</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">isdigit</span><span class="p">():</span>
             <span class="n">attr</span> <span class="o">=</span> <span class="n">attr</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>  <span class="c"># sNxxx only used for python, the name is stored without s-prefix</span>
-        <span class="n">seglist</span> <span class="o">=</span> <span class="p">[</span><span class="n">segment</span> <span class="k">for</span> <span class="n">segment</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_segments</span> <span class="k">if</span> <span class="n">segment</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">attr</span><span class="p">]</span>
+        <span class="n">seglist</span> <span class="o">=</span> <span class="p">[</span><span class="n">segment</span> <span class="k">for</span> <span class="n">segment</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">segments</span> <span class="k">if</span> <span class="n">segment</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">attr</span><span class="p">]</span>
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">seglist</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="k">return</span> <span class="nb">super</span><span class="p">(</span><span class="n">SegmentGroup</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__getattr__</span><span class="p">(</span><span class="n">attr</span><span class="p">)</span>
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">seglist</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
@@ -3395,7 +3533,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 
     <span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">return</span> <span class="s">&quot;&lt;SegmentGroup {segnames}&gt;&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
-            <span class="n">segnames</span><span class="o">=</span><span class="nb">repr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_segments</span><span class="p">))</span>
+            <span class="n">segnames</span><span class="o">=</span><span class="nb">repr</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">segments</span><span class="p">)))</span>
 
 </div>
 <div class="viewcode-block" id="Universe"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe">[docs]</a><span class="k">class</span> <span class="nc">Universe</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
@@ -3566,12 +3704,12 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">           control when unpickling instances of :class:`MDAnalysis.core.AtomGroup.AtomGroup`.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
 
-        <span class="kn">from</span> <span class="nn">..topology.core</span> <span class="kn">import</span> <span class="n">get_parser_for</span><span class="p">,</span> <span class="n">guess_format</span>
+        <span class="kn">from</span> <span class="nn">..topology.core</span> <span class="kn">import</span> <span class="n">get_parser_for</span>
         <span class="kn">from</span> <span class="nn">..topology.base</span> <span class="kn">import</span> <span class="n">TopologyReader</span>
         <span class="kn">from</span> <span class="nn">..coordinates.base</span> <span class="kn">import</span> <span class="n">ProtoReader</span>
 
         <span class="c"># managed attribute holding Reader</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">__trajectory</span> <span class="o">=</span> <span class="bp">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_trajectory</span> <span class="o">=</span> <span class="bp">None</span>
 
         <span class="c"># Cache is used to store objects which are built lazily into Universe</span>
         <span class="c"># Currently cached objects (managed property name and cache key):</span>
@@ -3610,8 +3748,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
                     <span class="n">coordinatefile</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filename</span>
             <span class="k">except</span> <span class="ne">TypeError</span><span class="p">:</span>
                 <span class="c"># or if file is known as a topology &amp; coordinate file, use that</span>
-                <span class="k">if</span> <span class="p">(</span><span class="n">guess_format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="n">fmt</span><span class="p">)</span> <span class="ow">in</span>
-                    <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">_topology_coordinates_readers</span><span class="p">):</span>
+                <span class="k">if</span> <span class="n">fmt</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+                    <span class="n">fmt</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">guess_format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">fmt</span> <span class="ow">in</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">_topology_coordinates_readers</span><span class="p">:</span>
                     <span class="n">coordinatefile</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filename</span>
             <span class="c"># Fix by SB: make sure coordinatefile is never an empty tuple</span>
             <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">coordinatefile</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
@@ -3626,7 +3765,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
                               <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;permissive_pdb_reader&#39;</span><span class="p">])</span>
             <span class="n">parser</span> <span class="o">=</span> <span class="n">get_parser_for</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">,</span>
                                     <span class="n">permissive</span><span class="o">=</span><span class="n">perm</span><span class="p">,</span>
-                                    <span class="n">tformat</span><span class="o">=</span><span class="n">topology_format</span><span class="p">)</span>
+                                    <span class="n">format</span><span class="o">=</span><span class="n">topology_format</span><span class="p">)</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="k">with</span> <span class="n">parser</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">,</span> <span class="n">universe</span><span class="o">=</span><span class="bp">self</span><span class="p">)</span> <span class="k">as</span> <span class="n">p</span><span class="p">:</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">_topology</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">parse</span><span class="p">()</span>
@@ -3691,34 +3830,41 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_topology</span><span class="p">[</span><span class="s">&#39;atoms&#39;</span><span class="p">])</span>
 
         <span class="c"># XXX: add H-bond information here if available from psf (or other sources)</span>
+
         <span class="c"># segment instant selectors</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_build_segments</span><span class="p">()</span>
 
     <span class="k">def</span> <span class="nf">_build_segments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Parse list of atoms into segments.</span>
 
-<span class="sd">        * updates :attr:`Universe.atoms` as a side effect</span>
-<span class="sd">        * updates :attr:`Universe.segments` and :attr:`Universe.residues`</span>
-<span class="sd">        * creates the segid instant selectors</span>
-
 <span class="sd">        Because of Python&#39;s syntax rules, attribute names cannot start with a</span>
 <span class="sd">        digit and so we prefix any segments starting with a digit with the</span>
 <span class="sd">        letter &#39;s&#39;. For instance, &#39;4AKE&#39; becomes the segid instant selector</span>
 <span class="sd">        &#39;s4AKE&#39;.</span>
+
+<span class="sd">        .. warning:: this method also sets convenience attributes for segment</span>
+<span class="sd">                     access from tne universe</span>
+
+<span class="sd">        :Returns:</span>
+<span class="sd">            *segments*</span>
+<span class="sd">                segment names modified with leading &#39;s&#39; characters if starting</span>
+<span class="sd">                with a digit</span>
+
+<span class="sd">        .. versionchanged:: 0.11.0</span>
+<span class="sd">           Now returns segment names, and does not modify ``self.atoms`` or</span>
+<span class="sd">           ``self.residues``</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="kn">from</span> <span class="nn">MDAnalysis.topology.core</span> <span class="kn">import</span> <span class="n">build_segments</span>
 
         <span class="n">segments</span> <span class="o">=</span> <span class="n">build_segments</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
-        <span class="k">for</span> <span class="n">seg</span> <span class="ow">in</span> <span class="n">segments</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
-            <span class="k">if</span> <span class="n">seg</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">isdigit</span><span class="p">():</span>
-                <span class="n">newsegname</span> <span class="o">=</span> <span class="s">&#39;s&#39;</span> <span class="o">+</span> <span class="n">seg</span>
-                <span class="n">segments</span><span class="p">[</span><span class="n">newsegname</span><span class="p">]</span> <span class="o">=</span> <span class="n">segments</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">seg</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">segments</span><span class="p">)</span>
-        <span class="c"># convenience access to residues and segments (these are managed attributes</span>
-        <span class="c"># (properties) and are built on the fly or read from a cache) -- does this</span>
-        <span class="c"># create memory problems?</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">segments</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">segments</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">residues</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">residues</span>
+        <span class="k">for</span> <span class="n">seg</span> <span class="ow">in</span> <span class="n">segments</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">seg</span><span class="o">.</span><span class="n">id</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">isdigit</span><span class="p">():</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="s">&#39;s&#39;</span> <span class="o">+</span> <span class="n">seg</span><span class="o">.</span><span class="n">id</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">seg</span><span class="o">.</span><span class="n">id</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">seg</span>
+
+        <span class="k">return</span> <span class="n">segments</span>
 
     <span class="k">def</span> <span class="nf">_init_top</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cat</span><span class="p">,</span> <span class="n">Top</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Initiate a generic form of topology.</span>
@@ -3747,7 +3893,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="nf">_init_bonds</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Set bond information from u._topology[&#39;bonds&#39;]</span>
 
-<span class="sd">        .. versionchanged 0.9.0</span>
+<span class="sd">        .. versionchanged:: 0.9.0</span>
 <span class="sd">           Now returns a :class:`~MDAnalysis.core.topologyobjects.TopologyGroup`</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">bonds</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_init_top</span><span class="p">(</span><span class="s">&#39;bonds&#39;</span><span class="p">,</span> <span class="n">top</span><span class="o">.</span><span class="n">Bond</span><span class="p">)</span>
@@ -3867,13 +4013,13 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;fragments&#39;</span><span class="p">)</span>
-<div class="viewcode-block" id="Universe.fragments"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.fragments">[docs]</a>    <span class="k">def</span> <span class="nf">fragments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">fragments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Read only tuple of fragments in the Universe</span>
 
 <span class="sd">        .. versionadded 0.9.0</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_init_fragments</span><span class="p">()</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;bondDict&#39;</span><span class="p">)</span>
     <span class="k">def</span> <span class="nf">_bondDict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -3992,6 +4138,14 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">if</span> <span class="s">&#39;impropers&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cache</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_cache</span><span class="p">[</span><span class="s">&#39;impropers&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_init_impropers</span><span class="p">()</span>
 </div>
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">residues</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">residues</span>
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">segments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">segments</span>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;bonds&#39;</span><span class="p">)</span>
     <span class="k">def</span> <span class="nf">bonds</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -4019,7 +4173,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_clear_caches</span><span class="p">(</span><span class="s">&#39;bondDict&#39;</span><span class="p">)</span>
 
     <span class="nd">@bonds.deleter</span>
-<div class="viewcode-block" id="Universe.bonds"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.bonds">[docs]</a>    <span class="k">def</span> <span class="nf">bonds</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">bonds</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Delete the bonds from Universe</span>
 
 <span class="sd">        This must also remove the per atom record of bonds (bondDict)</span>
@@ -4027,7 +4181,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">        .. versionadded:: 0.9.0</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_clear_caches</span><span class="p">(</span><span class="s">&#39;bonds&#39;</span><span class="p">,</span> <span class="s">&#39;bondDict&#39;</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;angles&#39;</span><span class="p">)</span>
     <span class="k">def</span> <span class="nf">angles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -4047,9 +4201,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_clear_caches</span><span class="p">(</span><span class="s">&#39;angleDict&#39;</span><span class="p">)</span>
 
     <span class="nd">@angles.deleter</span>
-<div class="viewcode-block" id="Universe.angles"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.angles">[docs]</a>    <span class="k">def</span> <span class="nf">angles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">angles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_clear_caches</span><span class="p">(</span><span class="s">&#39;angles&#39;</span><span class="p">,</span> <span class="s">&#39;angleDict&#39;</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;dihedrals&#39;</span><span class="p">)</span>
     <span class="k">def</span> <span class="nf">dihedrals</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -4069,9 +4223,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_clear_caches</span><span class="p">(</span><span class="s">&#39;dihedralDict&#39;</span><span class="p">)</span>
 
     <span class="nd">@dihedrals.deleter</span>
-<div class="viewcode-block" id="Universe.dihedrals"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.dihedrals">[docs]</a>    <span class="k">def</span> <span class="nf">dihedrals</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dihedrals</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_clear_caches</span><span class="p">(</span><span class="s">&#39;dihedrals&#39;</span><span class="p">,</span> <span class="s">&#39;dihedralDict&#39;</span><span class="p">)</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="nd">@cached</span><span class="p">(</span><span class="s">&#39;impropers&#39;</span><span class="p">)</span>
     <span class="k">def</span> <span class="nf">impropers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -4091,9 +4245,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_clear_caches</span><span class="p">(</span><span class="s">&#39;improperDict&#39;</span><span class="p">)</span>
 
     <span class="nd">@impropers.deleter</span>
-<div class="viewcode-block" id="Universe.impropers"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.impropers">[docs]</a>    <span class="k">def</span> <span class="nf">impropers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">impropers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_clear_caches</span><span class="p">(</span><span class="s">&#39;impropers&#39;</span><span class="p">,</span> <span class="s">&#39;improperDict&#39;</span><span class="p">)</span>
-</div>
+
 <div class="viewcode-block" id="Universe.load_new"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.load_new">[docs]</a>    <span class="k">def</span> <span class="nf">load_new</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Load coordinates from *filename*, using the suffix to detect file format.</span>
 
@@ -4143,12 +4297,20 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="n">reader_format</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;format&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
         <span class="n">perm</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;permissive&#39;</span><span class="p">,</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;permissive_pdb_reader&#39;</span><span class="p">])</span>
         <span class="n">reader</span> <span class="o">=</span> <span class="bp">None</span>
+
+        <span class="c"># Check if we were passed a Reader to use</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="k">if</span> <span class="n">reader_format</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="nb">issubclass</span><span class="p">(</span><span class="n">reader_format</span><span class="p">,</span> <span class="n">ProtoReader</span><span class="p">):</span>
                 <span class="n">reader</span> <span class="o">=</span> <span class="n">reader_format</span>
         <span class="k">except</span> <span class="ne">TypeError</span><span class="p">:</span>
             <span class="k">pass</span>
+
         <span class="k">if</span> <span class="ow">not</span> <span class="n">reader</span><span class="p">:</span>
+            <span class="c"># Check if we need to use Chain reader</span>
+            <span class="k">if</span> <span class="n">util</span><span class="o">.</span><span class="n">iterable</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
+                <span class="c"># Save the format and pass this to ChainReader</span>
+                <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s">&#39;format&#39;</span><span class="p">:</span> <span class="n">reader_format</span><span class="p">})</span>
+                <span class="n">reader_format</span><span class="o">=</span><span class="s">&#39;CHAIN&#39;</span>
             <span class="k">try</span><span class="p">:</span>
                 <span class="n">reader</span> <span class="o">=</span> <span class="n">get_reader_for</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span>
                                         <span class="n">permissive</span><span class="o">=</span><span class="n">perm</span><span class="p">,</span>
@@ -4157,10 +4319,9 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
                 <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span>
                     <span class="s">&quot;Cannot find an appropriate coordinate reader for file &#39;{0}&#39;.</span><span class="se">\n</span><span class="s">&quot;</span>
                     <span class="s">&quot;           {1}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">err</span><span class="p">))</span>
-                    <span class="c">#TypeError: ....&quot;</span>
-
         <span class="c"># supply number of atoms for readers that cannot do it for themselves</span>
         <span class="n">kwargs</span><span class="p">[</span><span class="s">&#39;n_atoms&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">n_atoms</span>
+
         <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span> <span class="o">=</span> <span class="n">reader</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>    <span class="c"># unified trajectory API</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">n_atoms</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">n_atoms</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">&quot;The topology and {form} trajectory files don&#39;t&quot;</span>
@@ -4343,16 +4504,16 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">dimensions</span>
 
     <span class="nd">@dimensions.setter</span>
-<div class="viewcode-block" id="Universe.dimensions"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.dimensions">[docs]</a>    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Set dimensions if the Timestep allows this</span>
 
 <span class="sd">        .. versionadded:: 0.9.0</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="c"># Add fancy error handling here or use Timestep?</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">dimensions</span> <span class="o">=</span> <span class="n">box</span>
-</div>
+
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Universe.coord"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.coord">[docs]</a>    <span class="k">def</span> <span class="nf">coord</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">coord</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Reference to current timestep and coordinates of universe.</span>
 
 <span class="sd">        The raw trajectory coordinates are :attr:`Universe.coord.positions`,</span>
@@ -4370,20 +4531,20 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
 <span class="sd">           :meth:`Universe.atoms.coordinates`.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">ts</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">trajectory</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Reference to trajectory reader object containing trajectory data.&quot;&quot;&quot;</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">__trajectory</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
-            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__trajectory</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_trajectory</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_trajectory</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s">&quot;No trajectory loaded into Universe&quot;</span><span class="p">)</span>
 
     <span class="nd">@trajectory.setter</span>
-<div class="viewcode-block" id="Universe.trajectory"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.trajectory">[docs]</a>    <span class="k">def</span> <span class="nf">trajectory</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
-        <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">__trajectory</span>  <span class="c"># guarantees that files are closed (?)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">__trajectory</span> <span class="o">=</span> <span class="n">value</span>
-</div>
+    <span class="k">def</span> <span class="nf">trajectory</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
+        <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">_trajectory</span>  <span class="c"># guarantees that files are closed (?)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_trajectory</span> <span class="o">=</span> <span class="n">value</span>
+
 <div class="viewcode-block" id="Universe.make_anchor"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.make_anchor">[docs]</a>    <span class="k">def</span> <span class="nf">make_anchor</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Add this Universe to the list where anchors are searched for when unpickling</span>
 <span class="sd">        :class:`MDAnalysis.core.AtomGroup.AtomGroup` instances. Silently proceeds if it</span>
@@ -4397,11 +4558,11 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
         <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">_anchor_universes</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
 </div>
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Universe.is_anchor"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.is_anchor">[docs]</a>    <span class="k">def</span> <span class="nf">is_anchor</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">is_anchor</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Whether this Universe will be checked for anchoring when unpickling</span>
 <span class="sd">        :class:`MDAnalysis.core.AtomGroup.AtomGroup` instances&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span> <span class="ow">in</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">_anchor_universes</span>
-</div>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">anchor_name</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_anchor_name</span>
@@ -4433,29 +4594,30 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
     <span class="c">#def __del__(self):</span>
     <span class="c">#    pass</span>
 </div>
-<div class="viewcode-block" id="asUniverse"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.asUniverse">[docs]</a><span class="k">def</span> <span class="nf">asUniverse</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="as_Universe"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.as_Universe">[docs]</a><span class="k">def</span> <span class="nf">as_Universe</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Return a universe from the input arguments.</span>
 
 <span class="sd">    1. If the first argument is a universe, just return it::</span>
 
-<span class="sd">         as_universe(universe) --&gt; universe</span>
+<span class="sd">         as_Universe(universe) --&gt; universe</span>
 
 <span class="sd">    2. Otherwise try to build a universe from the first or the first</span>
 <span class="sd">       and second argument::</span>
 
-<span class="sd">         asUniverse(PDB, **kwargs) --&gt; Universe(PDB, **kwargs)</span>
-<span class="sd">         asUniverse(PSF, DCD, **kwargs) --&gt; Universe(PSF, DCD, **kwargs)</span>
-<span class="sd">         asUniverse(*args, **kwargs) --&gt; Universe(*args, **kwargs)</span>
+<span class="sd">         as_Universe(PDB, **kwargs) --&gt; Universe(PDB, **kwargs)</span>
+<span class="sd">         as_Universe(PSF, DCD, **kwargs) --&gt; Universe(PSF, DCD, **kwargs)</span>
+<span class="sd">         as_Universe(*args, **kwargs) --&gt; Universe(*args, **kwargs)</span>
 
 <span class="sd">    :Returns: an instance of :class:`~MDAnalaysis.AtomGroup.Universe`</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-        <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">&quot;asUniverse() takes at least one argument (</span><span class="si">%d</span><span class="s"> given)&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">))</span>
+        <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">&quot;as_Universe() takes at least one argument (</span><span class="si">%d</span><span class="s"> given)&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">))</span>
     <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">Universe</span><span class="p">):</span>
         <span class="k">return</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
     <span class="k">return</span> <span class="n">Universe</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-
 </div>
+<span class="n">asUniverse</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">as_Universe</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;asUniverse&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;as_Universe&#39;</span><span class="p">)</span>
+
 <div class="viewcode-block" id="Merge"><a class="viewcode-back" href="../../../documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Merge">[docs]</a><span class="k">def</span> <span class="nf">Merge</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Return a :class:`Universe` from two or more :class:`AtomGroup` instances.</span>
 
@@ -4522,11 +4684,36 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
     <span class="n">atoms</span> <span class="o">=</span> <span class="p">[</span><span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">gr</span> <span class="ow">in</span> <span class="n">args</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">gr</span><span class="p">]</span>
     <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
         <span class="n">a</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">u</span>
+
     <span class="c"># adjust the atom numbering</span>
     <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">atoms</span><span class="p">):</span>
         <span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">i</span>
         <span class="n">a</span><span class="o">.</span><span class="n">serial</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span>
     <span class="n">u</span><span class="o">.</span><span class="n">atoms</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">atoms</span><span class="p">)</span>
+
+    <span class="c"># move over the topology</span>
+    <span class="n">offset</span> <span class="o">=</span> <span class="mi">0</span>
+    <span class="n">tops</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;bonds&#39;</span><span class="p">,</span> <span class="s">&#39;angles&#39;</span><span class="p">,</span> <span class="s">&#39;dihedrals&#39;</span><span class="p">,</span> <span class="s">&#39;impropers&#39;</span><span class="p">]</span>
+    <span class="n">idx_lists</span> <span class="o">=</span> <span class="p">{</span><span class="n">t</span><span class="p">:[]</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">tops</span><span class="p">}</span>
+    <span class="k">for</span> <span class="n">ag</span> <span class="ow">in</span> <span class="n">args</span><span class="p">:</span>
+        <span class="c"># create a mapping scheme for this atomgroup</span>
+        <span class="n">mapping</span> <span class="o">=</span> <span class="p">{</span><span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">:</span><span class="n">i</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">ag</span><span class="p">,</span> <span class="n">start</span><span class="o">=</span><span class="n">offset</span><span class="p">)}</span>
+        <span class="n">offset</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ag</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">tops</span><span class="p">:</span>
+            <span class="n">tg</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">ag</span><span class="p">,</span> <span class="n">t</span><span class="p">)</span>
+            <span class="c"># Create a topology group of only bonds that are within this ag</span>
+            <span class="c"># ie we don&#39;t want bonds that extend out of the atomgroup</span>
+            <span class="n">tg</span> <span class="o">=</span> <span class="n">tg</span><span class="o">.</span><span class="n">atomgroup_intersection</span><span class="p">(</span><span class="n">ag</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+
+            <span class="c"># Map them so they refer to our new indices</span>
+            <span class="n">new_idx</span> <span class="o">=</span> <span class="p">[</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span><span class="n">mapping</span><span class="p">[</span><span class="n">x</span><span class="p">],</span> <span class="n">entry</span><span class="p">))</span>
+                       <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">tg</span><span class="o">.</span><span class="n">to_indices</span><span class="p">()]</span>
+            <span class="n">idx_lists</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">new_idx</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">tops</span><span class="p">:</span>
+        <span class="n">u</span><span class="o">.</span><span class="n">_topology</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o">=</span> <span class="n">idx_lists</span><span class="p">[</span><span class="n">t</span><span class="p">]</span>
+
     <span class="c"># adjust the residue and segment numbering (removes any remaining references to the old universe)</span>
     <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">topology</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">build_residues</span><span class="p">(</span><span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
     <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">topology</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">build_segments</span><span class="p">(</span><span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
@@ -4539,7 +4726,7 @@ <h1>Source code for MDAnalysis.core.AtomGroup</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -4548,12 +4735,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -4563,7 +4749,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/core/Selection.html b/package/doc/html/_modules/MDAnalysis/core/Selection.html
index 7a234b01d92..4e8d4225a2e 100644
--- a/package/doc/html/_modules/MDAnalysis/core/Selection.html
+++ b/package/doc/html/_modules/MDAnalysis/core/Selection.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.core.Selection &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.core.Selection &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.core.Selection</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -105,9 +102,10 @@ <h1>Source code for MDAnalysis.core.Selection</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">re</span>
 <span class="kn">import</span> <span class="nn">numpy</span>
 <span class="kn">from</span> <span class="nn">numpy.lib.utils</span> <span class="kn">import</span> <span class="n">deprecate</span>
+<span class="kn">from</span> <span class="nn">Bio.KDTree</span> <span class="kn">import</span> <span class="n">KDTree</span>
+
 <span class="kn">from</span> <span class="nn">.AtomGroup</span> <span class="kn">import</span> <span class="n">AtomGroup</span><span class="p">,</span> <span class="n">Universe</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis.core</span> <span class="kn">import</span> <span class="n">flags</span>
-<span class="kn">from</span> <span class="nn">..lib.KDTree.NeighborSearch</span> <span class="kn">import</span> <span class="n">CoordinateNeighborSearch</span>
 <span class="kn">from</span> <span class="nn">..lib</span> <span class="kn">import</span> <span class="n">distances</span>
 <span class="kn">from</span> <span class="nn">..lib.mdamath</span> <span class="kn">import</span> <span class="n">triclinic_vectors</span>
 
@@ -239,16 +237,29 @@ <h1>Source code for MDAnalysis.core.Selection</h1><div class="highlight"><pre>
         <span class="sd">&quot;&quot;&quot;KDTree based selection is about 7x faster than distmat for typical problems.</span>
 <span class="sd">        Limitations: always ignores periodicity</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">sel_atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sel</span><span class="o">.</span><span class="n">_apply</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>  <span class="c"># group is wrong, should be universe (?!)</span>
-        <span class="n">sys_atoms_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_group_atoms</span> <span class="o">-</span> <span class="n">sel_atoms</span><span class="p">)]</span>  <span class="c"># list needed for back-indexing</span>
+        <span class="c"># group is wrong, should be universe (?!)</span>
+        <span class="n">sel_atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sel</span><span class="o">.</span><span class="n">_apply</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>
+        <span class="c"># list needed for back-indexing</span>
+        <span class="n">sys_atoms_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_group_atoms</span> <span class="o">-</span> <span class="n">sel_atoms</span><span class="p">)]</span>
         <span class="n">sel_indices</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">sel_atoms</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">int</span><span class="p">)</span>
         <span class="n">sys_indices</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">sys_atoms_list</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">int</span><span class="p">)</span>
         <span class="n">sel_coor</span> <span class="o">=</span> <span class="n">Selection</span><span class="o">.</span><span class="n">coord</span><span class="p">[</span><span class="n">sel_indices</span><span class="p">]</span>
-        <span class="n">sys_coor</span> <span class="o">=</span> <span class="n">Selection</span><span class="o">.</span><span class="n">coord</span><span class="p">[</span><span class="n">sys_indices</span><span class="p">]</span>
-        <span class="c"># Can we optimize search by using the larger set for the tree?</span>
-        <span class="n">CNS</span> <span class="o">=</span> <span class="n">CoordinateNeighborSearch</span><span class="p">(</span><span class="n">sys_coor</span><span class="p">)</span>  <span class="c"># cache the KDTree for this selection/frame?</span>
-        <span class="n">found_indices</span> <span class="o">=</span> <span class="n">CNS</span><span class="o">.</span><span class="n">search_list</span><span class="p">(</span><span class="n">sel_coor</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">cutoff</span><span class="p">)</span>
-        <span class="n">res_atoms</span> <span class="o">=</span> <span class="p">[</span><span class="n">sys_atoms_list</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">found_indices</span><span class="p">]</span>  <span class="c"># make list numpy array and use fancy indexing?</span>
+
+        <span class="n">kdtree</span> <span class="o">=</span> <span class="n">KDTree</span><span class="p">(</span><span class="n">dim</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">bucket_size</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
+        <span class="n">kdtree</span><span class="o">.</span><span class="n">set_coords</span><span class="p">(</span><span class="n">Selection</span><span class="o">.</span><span class="n">coord</span><span class="p">[</span><span class="n">sys_indices</span><span class="p">])</span>
+        <span class="n">found_indices</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">sel_coor</span><span class="p">):</span>
+            <span class="n">kdtree</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">cutoff</span><span class="p">)</span>
+            <span class="n">found_indices</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">kdtree</span><span class="o">.</span><span class="n">get_indices</span><span class="p">())</span>
+
+        <span class="c"># the list-comprehension here can be understood as a nested loop.</span>
+        <span class="c"># for list in found_indices:</span>
+        <span class="c">#     for i in list:</span>
+        <span class="c">#         yield sys_atoms_list[i]</span>
+        <span class="c"># converting found_indices to a numpy array won&#39;t reallt work since</span>
+        <span class="c"># each we will find a different number of neighbors for each center in</span>
+        <span class="c"># sel_coor.</span>
+        <span class="n">res_atoms</span> <span class="o">=</span> <span class="p">[</span><span class="n">sys_atoms_list</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="nb">list</span> <span class="ow">in</span> <span class="n">found_indices</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">]</span>
         <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="n">res_atoms</span><span class="p">)</span>
 
     <span class="k">def</span> <span class="nf">_apply_distmat</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">):</span>
@@ -291,26 +302,29 @@ <h1>Source code for MDAnalysis.core.Selection</h1><div class="highlight"><pre>
 
     <span class="k">def</span> <span class="nf">_apply_KDTree</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Selection using KDTree but periodic = True not supported.</span>
-<span class="sd">        (KDTree routine is ca 15% slower than the distance matrix one)</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">sys_indices</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_group_atoms_list</span><span class="p">])</span>
         <span class="n">sys_coor</span> <span class="o">=</span> <span class="n">Selection</span><span class="o">.</span><span class="n">coord</span><span class="p">[</span><span class="n">sys_indices</span><span class="p">]</span>
-        <span class="n">sel_atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sel</span><span class="o">.</span><span class="n">_apply</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>  <span class="c"># group is wrong, should be universe (?!)</span>
-        <span class="n">sel_CoG</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sel_atoms</span><span class="p">)</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">()</span>
+        <span class="c"># group is wrong, should be universe (?!)</span>
+        <span class="n">sel_atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sel</span><span class="o">.</span><span class="n">_apply</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>
+        <span class="n">sel_CoG</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sel_atoms</span><span class="p">)</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">ref</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">((</span><span class="n">sel_CoG</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">sel_CoG</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">sel_CoG</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">periodic</span><span class="p">:</span>
             <span class="k">pass</span>  <span class="c"># or warn? -- no periodic functionality with KDTree search</span>
+        <span class="n">kdtree</span> <span class="o">=</span> <span class="n">KDTree</span><span class="p">(</span><span class="n">dim</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">bucket_size</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
+        <span class="n">kdtree</span><span class="o">.</span><span class="n">set_coords</span><span class="p">(</span><span class="n">sys_coor</span><span class="p">)</span>
 
-        <span class="n">CNS</span> <span class="o">=</span> <span class="n">CoordinateNeighborSearch</span><span class="p">(</span><span class="n">sys_coor</span><span class="p">)</span>  <span class="c"># cache the KDTree for this selection/frame?</span>
-        <span class="n">found_ExtIndices</span> <span class="o">=</span> <span class="n">CNS</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ref</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">exRadius</span><span class="p">)</span>
-        <span class="n">found_IntIndices</span> <span class="o">=</span> <span class="n">CNS</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ref</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">inRadius</span><span class="p">)</span>
+        <span class="n">kdtree</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ref</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">exRadius</span><span class="p">)</span>
+        <span class="n">found_ExtIndices</span> <span class="o">=</span> <span class="n">kdtree</span><span class="o">.</span><span class="n">get_indices</span><span class="p">()</span>
+        <span class="n">kdtree</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ref</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">inRadius</span><span class="p">)</span>
+        <span class="n">found_IntIndices</span> <span class="o">=</span> <span class="n">kdtree</span><span class="o">.</span><span class="n">get_indices</span><span class="p">()</span>
         <span class="n">found_indices</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">found_ExtIndices</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">found_IntIndices</span><span class="p">))</span>
         <span class="n">res_atoms</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_group_atoms_list</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">found_indices</span><span class="p">]</span>
         <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="n">res_atoms</span><span class="p">)</span>
 
     <span class="k">def</span> <span class="nf">_apply_distmat</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">):</span>
         <span class="n">sel_atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sel</span><span class="o">.</span><span class="n">_apply</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>  <span class="c"># group is wrong, should be universe (?!)</span>
-        <span class="n">sel_CoG</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sel_atoms</span><span class="p">)</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">()</span>
+        <span class="n">sel_CoG</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sel_atoms</span><span class="p">)</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">()</span>
         <span class="n">sys_atoms_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_group_atoms</span><span class="p">)]</span>  <span class="c"># list needed for back-indexing</span>
         <span class="n">sys_ag</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sys_atoms_list</span><span class="p">)</span>
         <span class="n">sel_CoG_str</span> <span class="o">=</span> \
@@ -354,19 +368,21 @@ <h1>Source code for MDAnalysis.core.Selection</h1><div class="highlight"><pre>
         <span class="n">sys_indices</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_group_atoms_list</span><span class="p">])</span>
         <span class="n">sys_coor</span> <span class="o">=</span> <span class="n">Selection</span><span class="o">.</span><span class="n">coord</span><span class="p">[</span><span class="n">sys_indices</span><span class="p">]</span>
         <span class="n">sel_atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sel</span><span class="o">.</span><span class="n">_apply</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>  <span class="c"># group is wrong, should be universe (?!)</span>
-        <span class="n">sel_CoG</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sel_atoms</span><span class="p">)</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">()</span>
+        <span class="n">sel_CoG</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sel_atoms</span><span class="p">)</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">ref</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">((</span><span class="n">sel_CoG</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">sel_CoG</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">sel_CoG</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">periodic</span><span class="p">:</span>
             <span class="k">pass</span>  <span class="c"># or warn? -- no periodic functionality with KDTree search</span>
 
-        <span class="n">CNS</span> <span class="o">=</span> <span class="n">CoordinateNeighborSearch</span><span class="p">(</span><span class="n">sys_coor</span><span class="p">)</span>  <span class="c"># cache the KDTree for this selection/frame?</span>
-        <span class="n">found_indices</span> <span class="o">=</span> <span class="n">CNS</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ref</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">cutoff</span><span class="p">)</span>
-        <span class="n">res_atoms</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_group_atoms_list</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">found_indices</span><span class="p">]</span>  <span class="c"># make list numpy array and use fancy indexing?</span>
+        <span class="n">kdtree</span> <span class="o">=</span> <span class="n">KDTree</span><span class="p">(</span><span class="n">dim</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">bucket_size</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
+        <span class="n">kdtree</span><span class="o">.</span><span class="n">set_coords</span><span class="p">(</span><span class="n">sys_coor</span><span class="p">)</span>
+        <span class="n">kdtree</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ref</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">cutoff</span><span class="p">)</span>
+        <span class="n">found_indices</span> <span class="o">=</span> <span class="n">kdtree</span><span class="o">.</span><span class="n">get_indices</span><span class="p">()</span>
+        <span class="n">res_atoms</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_group_atoms_list</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">found_indices</span><span class="p">]</span>
         <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="n">res_atoms</span><span class="p">)</span>
 
     <span class="k">def</span> <span class="nf">_apply_distmat</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">):</span>
         <span class="n">sel_atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sel</span><span class="o">.</span><span class="n">_apply</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>  <span class="c"># group is wrong, should be universe (?!)</span>
-        <span class="n">sel_CoG</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sel_atoms</span><span class="p">)</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">()</span>
+        <span class="n">sel_CoG</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sel_atoms</span><span class="p">)</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">()</span>
         <span class="n">sys_atoms_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_group_atoms</span><span class="p">)]</span>  <span class="c"># list needed for back-indexing</span>
         <span class="n">sys_ag</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sys_atoms_list</span><span class="p">)</span>
         <span class="n">sel_CoG_str</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="s">&quot;point &quot;</span><span class="p">)</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sel_CoG</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">+</span> <span class="s">&quot; &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sel_CoG</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">+</span> <span class="s">&quot; &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sel_CoG</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="o">+</span> <span class="s">&quot; &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span>
@@ -399,7 +415,7 @@ <h1>Source code for MDAnalysis.core.Selection</h1><div class="highlight"><pre>
 
     <span class="k">def</span> <span class="nf">_apply_distmat</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">):</span>
         <span class="n">sel_atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sel</span><span class="o">.</span><span class="n">_apply</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>
-        <span class="n">sel_CoG</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sel_atoms</span><span class="p">)</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">()</span>
+        <span class="n">sel_CoG</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">sel_atoms</span><span class="p">)</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">()</span>
         <span class="n">coords</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">Selection</span><span class="o">.</span><span class="n">_group_atoms_list</span><span class="p">)</span><span class="o">.</span><span class="n">positions</span>
 
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">periodic</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">numpy</span><span class="o">.</span><span class="n">any</span><span class="p">(</span><span class="n">Selection</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">dimensions</span><span class="p">[:</span><span class="mi">3</span><span class="p">]</span><span class="o">==</span><span class="mi">0</span><span class="p">):</span>
@@ -413,17 +429,17 @@ <h1>Source code for MDAnalysis.core.Selection</h1><div class="highlight"><pre>
             <span class="n">cyl_z_hheight</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">zmax</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">zmin</span><span class="p">)</span><span class="o">/</span><span class="mi">2</span>
 
             <span class="k">if</span> <span class="mi">2</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">exRadius</span> <span class="o">&gt;</span> <span class="n">box</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
-                <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s">&quot;The diameter of the cylinder selection (</span><span class="si">%.3f</span><span class="s">) is larger than the unit cell&#39;s x dimension (</span><span class="si">%.3f</span><span class="s">). Can only do selections where it is smaller or equal.&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">exRadius</span><span class="p">,</span> <span class="n">box</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span> 
+                <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s">&quot;The diameter of the cylinder selection (</span><span class="si">%.3f</span><span class="s">) is larger than the unit cell&#39;s x dimension (</span><span class="si">%.3f</span><span class="s">). Can only do selections where it is smaller or equal.&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">exRadius</span><span class="p">,</span> <span class="n">box</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
             <span class="k">if</span> <span class="mi">2</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">exRadius</span> <span class="o">&gt;</span> <span class="n">box</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
                 <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s">&quot;The diameter of the cylinder selection (</span><span class="si">%.3f</span><span class="s">) is larger than the unit cell&#39;s y dimension (</span><span class="si">%.3f</span><span class="s">). Can only do selections where it is smaller or equal.&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">exRadius</span><span class="p">,</span> <span class="n">box</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
             <span class="k">if</span> <span class="mi">2</span><span class="o">*</span><span class="n">cyl_z_hheight</span> <span class="o">&gt;</span> <span class="n">box</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span>
                 <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s">&quot;The total length of the cylinder selection in z (</span><span class="si">%.3f</span><span class="s">) is larger than the unit cell&#39;s z dimension (</span><span class="si">%.3f</span><span class="s">). Can only do selections where it is smaller or equal.&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">cyl_z_hheight</span><span class="p">,</span> <span class="n">box</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span>
             <span class="c">#how off-center in z is our CoG relative to the cylinder&#39;s center</span>
             <span class="n">cyl_center</span> <span class="o">=</span> <span class="n">sel_CoG</span> <span class="o">+</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,(</span><span class="bp">self</span><span class="o">.</span><span class="n">zmax</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">zmin</span><span class="p">)</span><span class="o">/</span><span class="mi">2</span><span class="p">]</span>
-            <span class="n">coords</span> <span class="o">+=</span> <span class="n">box</span><span class="o">/</span><span class="mi">2</span> <span class="o">-</span> <span class="n">cyl_center</span> 
-            <span class="n">coords</span> <span class="o">=</span> <span class="n">distances</span><span class="o">.</span><span class="n">applyPBC</span><span class="p">(</span><span class="n">coords</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="n">Selection</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">dimensions</span><span class="p">)</span>
+            <span class="n">coords</span> <span class="o">+=</span> <span class="n">box</span><span class="o">/</span><span class="mi">2</span> <span class="o">-</span> <span class="n">cyl_center</span>
+            <span class="n">coords</span> <span class="o">=</span> <span class="n">distances</span><span class="o">.</span><span class="n">apply_PBC</span><span class="p">(</span><span class="n">coords</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="n">Selection</span><span class="o">.</span><span class="n">coord</span><span class="o">.</span><span class="n">dimensions</span><span class="p">)</span>
             <span class="k">if</span> <span class="n">is_triclinic</span><span class="p">:</span>
-                <span class="n">coords</span> <span class="o">=</span> <span class="n">distances</span><span class="o">.</span><span class="n">applyPBC</span><span class="p">(</span><span class="n">coords</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">)</span>
+                <span class="n">coords</span> <span class="o">=</span> <span class="n">distances</span><span class="o">.</span><span class="n">apply_PBC</span><span class="p">(</span><span class="n">coords</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">)</span>
             <span class="n">sel_CoG</span> <span class="o">=</span> <span class="n">box</span><span class="o">/</span><span class="mi">2</span>
             <span class="n">zmin</span> <span class="o">=</span> <span class="o">-</span><span class="n">cyl_z_hheight</span>
             <span class="n">zmax</span> <span class="o">=</span> <span class="n">cyl_z_hheight</span>
@@ -456,7 +472,7 @@ <h1>Source code for MDAnalysis.core.Selection</h1><div class="highlight"><pre>
 <span class="k">class</span> <span class="nc">CylindricalZoneSelection</span><span class="p">(</span><span class="n">_CylindricalSelection</span><span class="p">):</span>
     <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sel</span><span class="p">,</span> <span class="n">exRadius</span><span class="p">,</span> <span class="n">zmax</span><span class="p">,</span> <span class="n">zmin</span><span class="p">,</span> <span class="n">periodic</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
         <span class="n">Selection</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
-        <span class="n">_CylindricalSelection</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sel</span><span class="p">,</span> <span class="n">exRadius</span><span class="p">,</span> <span class="n">zmax</span><span class="p">,</span> <span class="n">zmin</span><span class="p">,</span> <span class="n">periodic</span><span class="p">)</span> 
+        <span class="n">_CylindricalSelection</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sel</span><span class="p">,</span> <span class="n">exRadius</span><span class="p">,</span> <span class="n">zmax</span><span class="p">,</span> <span class="n">zmin</span><span class="p">,</span> <span class="n">periodic</span><span class="p">)</span>
 
     <span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">return</span> <span class="s">&quot;&lt;&#39;CylindricalZoneSelection&#39; radius &quot;</span> <span class="o">+</span> <span class="nb">repr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">exRadius</span><span class="p">)</span> <span class="o">+</span> <span class="s">&quot;, zmax &quot;</span> <span class="o">+</span> <span class="nb">repr</span><span class="p">(</span>
@@ -465,7 +481,7 @@ <h1>Source code for MDAnalysis.core.Selection</h1><div class="highlight"><pre>
 <span class="k">class</span> <span class="nc">CylindricalLayerSelection</span><span class="p">(</span><span class="n">_CylindricalSelection</span><span class="p">):</span>
     <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sel</span><span class="p">,</span> <span class="n">inRadius</span><span class="p">,</span> <span class="n">exRadius</span><span class="p">,</span> <span class="n">zmax</span><span class="p">,</span> <span class="n">zmin</span><span class="p">,</span> <span class="n">periodic</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
         <span class="n">Selection</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
-        <span class="n">_CylindricalSelection</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sel</span><span class="p">,</span> <span class="n">exRadius</span><span class="p">,</span> <span class="n">zmax</span><span class="p">,</span> <span class="n">zmin</span><span class="p">,</span> <span class="n">periodic</span><span class="p">)</span> 
+        <span class="n">_CylindricalSelection</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sel</span><span class="p">,</span> <span class="n">exRadius</span><span class="p">,</span> <span class="n">zmax</span><span class="p">,</span> <span class="n">zmin</span><span class="p">,</span> <span class="n">periodic</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">inRadius</span> <span class="o">=</span> <span class="n">inRadius</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">inRadiusSq</span> <span class="o">=</span> <span class="n">inRadius</span> <span class="o">*</span> <span class="n">inRadius</span>
 
@@ -1192,7 +1208,7 @@ <h1>Source code for MDAnalysis.core.Selection</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1201,12 +1217,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1216,7 +1231,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/core/Timeseries.html b/package/doc/html/_modules/MDAnalysis/core/Timeseries.html
index acfceca527d..9deba273a91 100644
--- a/package/doc/html/_modules/MDAnalysis/core/Timeseries.html
+++ b/package/doc/html/_modules/MDAnalysis/core/Timeseries.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.core.Timeseries &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.core.Timeseries &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.core.Timeseries</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -259,10 +256,10 @@ <h1>Source code for MDAnalysis.core.Timeseries</h1><div class="highlight"><pre>
 
     <span class="c"># Properties</span>
     <span class="nd">@property</span>
-<div class="viewcode-block" id="Timeseries.shape"><a class="viewcode-back" href="../../../documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.Timeseries.shape">[docs]</a>    <span class="k">def</span> <span class="nf">shape</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">shape</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;shape tuple of the underlying numpy array&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__data__</span><span class="o">.</span><span class="n">shape</span>
-</div>
+
     <span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__data__</span><span class="p">[</span><span class="n">item</span><span class="p">]</span>
 
@@ -481,7 +478,7 @@ <h1>Source code for MDAnalysis.core.Timeseries</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -490,12 +487,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -505,7 +501,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/core/__init__.html b/package/doc/html/_modules/MDAnalysis/core/__init__.html
index 808e6787cc6..5eccb6912af 100644
--- a/package/doc/html/_modules/MDAnalysis/core/__init__.html
+++ b/package/doc/html/_modules/MDAnalysis/core/__init__.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.core.__init__ &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.core.__init__ &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.core.__init__</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -112,13 +109,13 @@ <h1>Source code for MDAnalysis.core.__init__</h1><div class="highlight"><pre>
 
 <span class="sd">  water_shell = u.select_atoms(&#39;name OH2 and around 4.0 protein&#39;)</span>
 <span class="sd">  water_shell.n_atoms           # how many waters were selected</span>
-<span class="sd">  water_shell.totalMass()       # their total mass</span>
+<span class="sd">  water_shell.total_mass()       # their total mass</span>
 
 <span class="sd">:class:`AtomGroup` instances have various methods that allow</span>
 <span class="sd">calculation of simple properties. For more complicated analysis,</span>
 <span class="sd">obtain the coordinates as a numpy array ::</span>
 
-<span class="sd">  coords = water_shell.coordinates()</span>
+<span class="sd">  coords = water_shell.positions</span>
 
 <span class="sd">and write your own Python code.</span>
 
@@ -503,8 +500,8 @@ <h1>Source code for MDAnalysis.core.__init__</h1><div class="highlight"><pre>
 
 <span class="sd">           Changing this to ``True`` changes the default behaviour of</span>
 <span class="sd">           commonly used :class:`MDAnalysis.core.AtomGroup.AtomGroup` methods</span>
-<span class="sd">           such as :meth:`MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass`</span>
-<span class="sd">           and :meth:`MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry`!</span>
+<span class="sd">           such as :meth:`MDAnalysis.core.AtomGroup.AtomGroup.center_of_mass`</span>
+<span class="sd">           and :meth:`MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry`!</span>
 <span class="sd">        &quot;&quot;&quot;</span><span class="p">),</span>
 
 <span class="p">]</span>
@@ -530,7 +527,7 @@ <h1>Source code for MDAnalysis.core.__init__</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -539,12 +536,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -554,7 +550,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/exceptions.html b/package/doc/html/_modules/MDAnalysis/exceptions.html
index 5db4e599f33..0a8d3de1c78 100644
--- a/package/doc/html/_modules/MDAnalysis/exceptions.html
+++ b/package/doc/html/_modules/MDAnalysis/exceptions.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.exceptions &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.exceptions &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
+    <link rel="up" title="Module code" href="../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.exceptions</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -96,19 +93,19 @@ <h1>Source code for MDAnalysis.exceptions</h1><div class="highlight"><pre>
 
 <span class="sd">&quot;&quot;&quot;</span>
 
-<div class="viewcode-block" id="SelectionError"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.exceptions.SelectionError">[docs]</a><span class="k">class</span> <span class="nc">SelectionError</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
+<div class="viewcode-block" id="SelectionError"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.analysis.hole.SelectionError">[docs]</a><span class="k">class</span> <span class="nc">SelectionError</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Raised when a atom selection failed.&quot;&quot;&quot;</span>
 
 </div>
-<div class="viewcode-block" id="FinishTimeException"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.exceptions.FinishTimeException">[docs]</a><span class="k">class</span> <span class="nc">FinishTimeException</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
+<div class="viewcode-block" id="FinishTimeException"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.analysis.hole.FinishTimeException">[docs]</a><span class="k">class</span> <span class="nc">FinishTimeException</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;For Issue 188.&quot;&quot;&quot;</span>
 
 </div>
-<div class="viewcode-block" id="NoDataError"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.exceptions.NoDataError">[docs]</a><span class="k">class</span> <span class="nc">NoDataError</span><span class="p">(</span><span class="ne">ValueError</span><span class="p">):</span>
+<div class="viewcode-block" id="NoDataError"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.analysis.hole.NoDataError">[docs]</a><span class="k">class</span> <span class="nc">NoDataError</span><span class="p">(</span><span class="ne">ValueError</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Raised when empty input is not allowed or required data are missing.&quot;&quot;&quot;</span>
 
 </div>
-<div class="viewcode-block" id="ApplicationError"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.exceptions.ApplicationError">[docs]</a><span class="k">class</span> <span class="nc">ApplicationError</span><span class="p">(</span><span class="ne">OSError</span><span class="p">):</span>
+<div class="viewcode-block" id="ApplicationError"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.analysis.hole.ApplicationError">[docs]</a><span class="k">class</span> <span class="nc">ApplicationError</span><span class="p">(</span><span class="ne">OSError</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Raised when an external application failed.</span>
 
 <span class="sd">    The error code is specific for the application.</span>
@@ -117,23 +114,23 @@ <h1>Source code for MDAnalysis.exceptions</h1><div class="highlight"><pre>
 <span class="sd">    &quot;&quot;&quot;</span>
 
 </div>
-<div class="viewcode-block" id="SelectionWarning"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.exceptions.SelectionWarning">[docs]</a><span class="k">class</span> <span class="nc">SelectionWarning</span><span class="p">(</span><span class="ne">Warning</span><span class="p">):</span>
+<div class="viewcode-block" id="SelectionWarning"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.analysis.hole.SelectionWarning">[docs]</a><span class="k">class</span> <span class="nc">SelectionWarning</span><span class="p">(</span><span class="ne">Warning</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Warning indicating a possible problem with a selection.&quot;&quot;&quot;</span>
 
 </div>
-<div class="viewcode-block" id="MissingDataWarning"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.exceptions.MissingDataWarning">[docs]</a><span class="k">class</span> <span class="nc">MissingDataWarning</span><span class="p">(</span><span class="ne">Warning</span><span class="p">):</span>
+<div class="viewcode-block" id="MissingDataWarning"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.analysis.hole.MissingDataWarning">[docs]</a><span class="k">class</span> <span class="nc">MissingDataWarning</span><span class="p">(</span><span class="ne">Warning</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Warning indicating is that required data are missing.&quot;&quot;&quot;</span>
 
 </div>
-<div class="viewcode-block" id="ConversionWarning"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.exceptions.ConversionWarning">[docs]</a><span class="k">class</span> <span class="nc">ConversionWarning</span><span class="p">(</span><span class="ne">Warning</span><span class="p">):</span>
+<div class="viewcode-block" id="ConversionWarning"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.analysis.hole.ConversionWarning">[docs]</a><span class="k">class</span> <span class="nc">ConversionWarning</span><span class="p">(</span><span class="ne">Warning</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Warning indicating a problem with converting between units.&quot;&quot;&quot;</span>
 
 </div>
-<div class="viewcode-block" id="FileFormatWarning"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.exceptions.FileFormatWarning">[docs]</a><span class="k">class</span> <span class="nc">FileFormatWarning</span><span class="p">(</span><span class="ne">Warning</span><span class="p">):</span>
+<div class="viewcode-block" id="FileFormatWarning"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.analysis.hole.FileFormatWarning">[docs]</a><span class="k">class</span> <span class="nc">FileFormatWarning</span><span class="p">(</span><span class="ne">Warning</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Warning indicating possible problems with a file format.&quot;&quot;&quot;</span>
 
 </div>
-<div class="viewcode-block" id="StreamWarning"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.exceptions.StreamWarning">[docs]</a><span class="k">class</span> <span class="nc">StreamWarning</span><span class="p">(</span><span class="ne">Warning</span><span class="p">):</span>
+<div class="viewcode-block" id="StreamWarning"><a class="viewcode-back" href="../../documentation_pages/exceptions.html#MDAnalysis.analysis.hole.StreamWarning">[docs]</a><span class="k">class</span> <span class="nc">StreamWarning</span><span class="p">(</span><span class="ne">Warning</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Warning indicating a possible problem with a stream.</span>
 
 <span class="sd">    :exc:`StreamWarning` is used when streams are substituted for simple access</span>
@@ -148,7 +145,7 @@ <h1>Source code for MDAnalysis.exceptions</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -157,12 +154,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -172,7 +168,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/lib/NeighborSearch.html b/package/doc/html/_modules/MDAnalysis/lib/NeighborSearch.html
new file mode 100644
index 00000000000..ff44678c3a2
--- /dev/null
+++ b/package/doc/html/_modules/MDAnalysis/lib/NeighborSearch.html
@@ -0,0 +1,209 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>MDAnalysis.lib.NeighborSearch &mdash; MDAnalysis 0.11.0 documentation</title>
+    
+    <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
+    <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../../../',
+        VERSION:     '0.11.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="../../../_static/jquery.js"></script>
+    <script type="text/javascript" src="../../../_static/underscore.js"></script>
+    <script type="text/javascript" src="../../../_static/doctools.js"></script>
+    <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <link rel="search" type="application/opensearchdescription+xml"
+          title="Search within MDAnalysis 0.11.0 documentation"
+          href="../../../_static/opensearch.xml"/>
+    <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
+  </head>
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../../../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="../../../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
+      </ul>
+    </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+            <p class="logo"><a href="../../../index.html">
+              <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
+            </a></p>
+<div id="searchbox" style="display: none" role="search">
+  <h3>Quick search</h3>
+    <form class="search" action="../../../search.html" method="get">
+      <input type="text" name="q" />
+      <input type="submit" value="Go" />
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+    <p class="searchtip" style="font-size: 90%">
+    Enter search terms or a module, class or function name.
+    </p>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <h1>Source code for MDAnalysis.lib.NeighborSearch</h1><div class="highlight"><pre>
+<span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
+<span class="c"># vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8</span>
+<span class="c">#</span>
+<span class="c"># MDAnalysis --- http://www.MDAnalysis.org</span>
+<span class="c"># Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein</span>
+<span class="c"># and contributors (see AUTHORS for the full list)</span>
+<span class="c">#</span>
+<span class="c"># Released under the GNU Public Licence, v2 or any higher version</span>
+<span class="c">#</span>
+<span class="c"># Please cite your use of MDAnalysis in published work:</span>
+<span class="c">#</span>
+<span class="c"># N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.</span>
+<span class="c"># MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.</span>
+<span class="c"># J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787</span>
+<span class="c">#</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">Neighbor Search wrapper for MDAnalysis --- :mod: `MDAnalysis.lib.NeighborSearch`</span>
+<span class="sd">===============================================================================</span>
+
+<span class="sd">This module contains classes that allow neighbor searches directly with</span>
+<span class="sd">`AtomGroup` objects from `MDAnalysis`.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">import</span> <span class="nn">numpy</span>
+<span class="kn">from</span> <span class="nn">Bio.KDTree</span> <span class="kn">import</span> <span class="n">KDTree</span>
+
+<span class="kn">from</span> <span class="nn">MDAnalysis.core.AtomGroup</span> <span class="kn">import</span> <span class="n">AtomGroup</span>
+
+
+<div class="viewcode-block" id="AtomNeighborSearch"><a class="viewcode-back" href="../../../documentation_pages/lib/NeighborSearch.html#MDAnalysis.lib.NeighborSearch.AtomNeighborSearch">[docs]</a><span class="k">class</span> <span class="nc">AtomNeighborSearch</span><span class="p">():</span>
+    <span class="sd">&quot;&quot;&quot;This class can be used to find all atoms/residues/segements within the</span>
+<span class="sd">    radius of a given query position.</span>
+
+<span class="sd">    This class is using the BioPython KDTree for the neighborsearch. This class</span>
+<span class="sd">    also does not apply PBC to the distance calculattions. So you have to ensure</span>
+<span class="sd">    yourself that the trajectory has been corrected for PBC artifacts.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom_group</span><span class="p">,</span> <span class="n">bucket_size</span><span class="o">=</span><span class="mi">10</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        :Arguments:</span>
+<span class="sd">         *atom_list*</span>
+<span class="sd">          list of atoms (:class: `~MDAnalysis.core.AtomGroup.AtomGroup`)</span>
+<span class="sd">         *bucket_size*</span>
+<span class="sd">          Number of entries in leafs of the KDTree. If you suffer poor</span>
+<span class="sd">          performance you can play around with this number. Increasing the</span>
+<span class="sd">          `bucket_size` will speed up the construction of the KDTree but</span>
+<span class="sd">          slow down the search.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">atom_group</span> <span class="o">=</span> <span class="n">atom_group</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">atom_group</span><span class="p">,</span> <span class="s">&#39;coordinates&#39;</span><span class="p">):</span>
+            <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">&#39;atom_group must have a coordinates() method&#39;</span>
+                            <span class="s">&#39;(eq a AtomGroup from a selection)&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">kdtree</span> <span class="o">=</span> <span class="n">KDTree</span><span class="p">(</span><span class="n">dim</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">bucket_size</span><span class="o">=</span><span class="n">bucket_size</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">kdtree</span><span class="o">.</span><span class="n">set_coords</span><span class="p">(</span><span class="n">atom_group</span><span class="o">.</span><span class="n">coordinates</span><span class="p">())</span>
+
+<div class="viewcode-block" id="AtomNeighborSearch.search"><a class="viewcode-back" href="../../../documentation_pages/lib/NeighborSearch.html#MDAnalysis.lib.NeighborSearch.AtomNeighborSearch.search">[docs]</a>    <span class="k">def</span> <span class="nf">search</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atoms</span><span class="p">,</span> <span class="n">radius</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="s">&#39;A&#39;</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Return all atoms/residues/segments that are within *radius* of the</span>
+<span class="sd">        atoms in *atoms*.</span>
+
+<span class="sd">        :Arguments:</span>
+<span class="sd">         *atoms*</span>
+<span class="sd">          list of atoms (:class: `~MDAnalysis.core.AtomGroup.AtomGroup`)</span>
+<span class="sd">         *radius*</span>
+<span class="sd">          float. Radius for search in Angstrom.</span>
+<span class="sd">         *level* (optional)</span>
+<span class="sd">          char (A, R, S). Return atoms(A), residues(R) or segments(S) within</span>
+<span class="sd">          *radius* of *atoms*.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">indices</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">atoms</span><span class="o">.</span><span class="n">coordinates</span><span class="p">():</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">kdtree</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="n">radius</span><span class="p">)</span>
+            <span class="n">indices</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">kdtree</span><span class="o">.</span><span class="n">get_indices</span><span class="p">())</span>
+        <span class="n">unique_idx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">unique</span><span class="p">([</span><span class="n">i</span> <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">indices</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">l</span><span class="p">])</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_index2level</span><span class="p">(</span><span class="n">unique_idx</span><span class="p">,</span> <span class="n">level</span><span class="p">)</span>
+</div>
+    <span class="k">def</span> <span class="nf">_index2level</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">indices</span><span class="p">,</span> <span class="n">level</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot; Convert list of atom_indices in a AtomGroup to either the</span>
+<span class="sd">            Atoms or segments/residues containing these atoms.</span>
+
+<span class="sd">        :Arguments:</span>
+<span class="sd">         *indices*</span>
+<span class="sd">           list of atom indices</span>
+<span class="sd">         *level*</span>
+<span class="sd">          char (A, R, S). Return atoms(A), residues(R) or segments(S) within</span>
+<span class="sd">          *radius* of *atoms*.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">n_atom_list</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_group</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">indices</span><span class="p">]</span>
+        <span class="k">if</span> <span class="n">level</span> <span class="o">==</span> <span class="s">&#39;A&#39;</span><span class="p">:</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">n_atom_list</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+                <span class="k">return</span> <span class="p">[]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="k">return</span> <span class="n">AtomGroup</span><span class="p">(</span><span class="n">n_atom_list</span><span class="p">)</span>
+        <span class="k">elif</span> <span class="n">level</span> <span class="o">==</span> <span class="s">&#39;R&#39;</span><span class="p">:</span>
+            <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">residue</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">n_atom_list</span><span class="p">]))</span>
+        <span class="k">elif</span> <span class="n">level</span> <span class="o">==</span> <span class="s">&#39;S&#39;</span><span class="p">:</span>
+            <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">segment</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">n_atom_list</span><span class="p">]))</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s">&#39;{}: level not implemented&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">level</span><span class="p">))</span></div>
+</pre></div>
+
+          </div>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../../../genindex.html" title="General Index"
+             >index</a></li>
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+          <a href="../../../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
+    Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
+    David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
+    Lennard van der Feltz, Philip Fowler, Joseph Goose, Richard J. Gowers, Lukas Grossar,
+    Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon, Alex Nesterenko,
+    Manuel Nuno Melo, Caio S. Souza, Danny Parton, Joshua L. Phillips, Tyler Reddy,
+    Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
+    Zhuyi Xue, Carlos Yáñez S.,
+    and Oliver Beckstein.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
+    </div>
+  </body>
+</html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/lib/distances.html b/package/doc/html/_modules/MDAnalysis/lib/distances.html
index 97a11748cc0..c5a169a57a8 100644
--- a/package/doc/html/_modules/MDAnalysis/lib/distances.html
+++ b/package/doc/html/_modules/MDAnalysis/lib/distances.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.lib.distances &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.lib.distances &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
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@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
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               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*-</span>
@@ -106,11 +103,12 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
 <span class="sd">.. autofunction:: calc_bonds(atom1, atom2 [, box, [,result]])</span>
 <span class="sd">.. autofunction:: calc_angles(atom1, atom2, atom3 [,box [, result]])</span>
 <span class="sd">.. autofunction:: calc_dihedrals(atom1, atom2, atom3, atom4 [,box [, result]])</span>
-<span class="sd">.. autofunction:: applyPBC(coordinates, box)</span>
+<span class="sd">.. autofunction:: apply_PBC(coordinates, box)</span>
 <span class="sd">.. autofunction:: transform_RtoS(coordinates, box)</span>
 <span class="sd">.. autofunction:: transform_StoR(coordinates, box)</span>
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
+<span class="kn">from</span> <span class="nn">numpy.lib.utils</span> <span class="kn">import</span> <span class="n">deprecate</span>
 
 <span class="kn">from</span> <span class="nn">.mdamath</span> <span class="kn">import</span> <span class="n">triclinic_vectors</span><span class="p">,</span> <span class="n">triclinic_box</span>
 <span class="kn">from</span> <span class="nn">._distances</span> <span class="kn">import</span> <span class="p">(</span><span class="n">calc_distance_array</span><span class="p">,</span>
@@ -213,7 +211,7 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
         <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">&quot;Input arrays must all be same shape&quot;</span>
                          <span class="s">&quot;Got {0}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">shape</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">arrays</span><span class="p">]))</span>
 
-<div class="viewcode-block" id="distance_array"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.lib.distances.distance_array">[docs]</a><span class="k">def</span> <span class="nf">distance_array</span><span class="p">(</span><span class="n">reference</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">result</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+<div class="viewcode-block" id="distance_array"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.analysis.distances.distance_array">[docs]</a><span class="k">def</span> <span class="nf">distance_array</span><span class="p">(</span><span class="n">reference</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">result</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Calculate all distances between a reference set and another configuration.</span>
 
 <span class="sd">    If there are *i* positions in reference, and *j* positions in configuration,</span>
@@ -285,7 +283,7 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">distances</span>
 
 </div>
-<div class="viewcode-block" id="self_distance_array"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.lib.distances.self_distance_array">[docs]</a><span class="k">def</span> <span class="nf">self_distance_array</span><span class="p">(</span><span class="n">reference</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">result</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+<div class="viewcode-block" id="self_distance_array"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.analysis.distances.self_distance_array">[docs]</a><span class="k">def</span> <span class="nf">self_distance_array</span><span class="p">(</span><span class="n">reference</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">result</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Calculate all distances within a configuration *reference*.</span>
 
 <span class="sd">    If a *box* is supplied then a minimum image convention is used before</span>
@@ -355,7 +353,7 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">distances</span>
 
 </div>
-<div class="viewcode-block" id="transform_RtoS"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.lib.distances.transform_RtoS">[docs]</a><span class="k">def</span> <span class="nf">transform_RtoS</span><span class="p">(</span><span class="n">inputcoords</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
+<div class="viewcode-block" id="transform_RtoS"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.analysis.distances.transform_RtoS">[docs]</a><span class="k">def</span> <span class="nf">transform_RtoS</span><span class="p">(</span><span class="n">inputcoords</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Transform an array of coordinates from real space to S space (aka lambda space)</span>
 
 <span class="sd">    S space represents fractional space within the unit cell for this system</span>
@@ -398,7 +396,7 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">coords</span>
 
 </div>
-<div class="viewcode-block" id="transform_StoR"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.lib.distances.transform_StoR">[docs]</a><span class="k">def</span> <span class="nf">transform_StoR</span><span class="p">(</span><span class="n">inputcoords</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
+<div class="viewcode-block" id="transform_StoR"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.analysis.distances.transform_StoR">[docs]</a><span class="k">def</span> <span class="nf">transform_StoR</span><span class="p">(</span><span class="n">inputcoords</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Transform an array of coordinates from S space into real space.</span>
 
 <span class="sd">    S space represents fractional space within the unit cell for this system</span>
@@ -435,7 +433,7 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">coords</span>
 
 </div>
-<div class="viewcode-block" id="calc_bonds"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.lib.distances.calc_bonds">[docs]</a><span class="k">def</span> <span class="nf">calc_bonds</span><span class="p">(</span><span class="n">coords1</span><span class="p">,</span> <span class="n">coords2</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">result</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+<div class="viewcode-block" id="calc_bonds"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.analysis.distances.calc_bonds">[docs]</a><span class="k">def</span> <span class="nf">calc_bonds</span><span class="p">(</span><span class="n">coords1</span><span class="p">,</span> <span class="n">coords2</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">result</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Calculate all distances between a pair of atoms.  *atom1* and *atom2* are both</span>
 <span class="sd">    arrays of coordinates, where atom1[i] and atom2[i] represent a bond.</span>
@@ -510,7 +508,7 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">distances</span>
 
 </div>
-<div class="viewcode-block" id="calc_angles"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.lib.distances.calc_angles">[docs]</a><span class="k">def</span> <span class="nf">calc_angles</span><span class="p">(</span><span class="n">coords1</span><span class="p">,</span> <span class="n">coords2</span><span class="p">,</span> <span class="n">coords3</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">result</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+<div class="viewcode-block" id="calc_angles"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.analysis.distances.calc_angles">[docs]</a><span class="k">def</span> <span class="nf">calc_angles</span><span class="p">(</span><span class="n">coords1</span><span class="p">,</span> <span class="n">coords2</span><span class="p">,</span> <span class="n">coords3</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">result</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Calculates the angle formed between three atoms, over a list of coordinates.</span>
 <span class="sd">    All *atom* inputs are lists of coordinates of equal length, with *atom2*</span>
@@ -587,7 +585,7 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">angles</span>
 
 </div>
-<div class="viewcode-block" id="calc_dihedrals"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.lib.distances.calc_dihedrals">[docs]</a><span class="k">def</span> <span class="nf">calc_dihedrals</span><span class="p">(</span><span class="n">coords1</span><span class="p">,</span> <span class="n">coords2</span><span class="p">,</span> <span class="n">coords3</span><span class="p">,</span> <span class="n">coords4</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">result</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+<div class="viewcode-block" id="calc_dihedrals"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.analysis.distances.calc_dihedrals">[docs]</a><span class="k">def</span> <span class="nf">calc_dihedrals</span><span class="p">(</span><span class="n">coords1</span><span class="p">,</span> <span class="n">coords2</span><span class="p">,</span> <span class="n">coords3</span><span class="p">,</span> <span class="n">coords4</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">result</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Calculate the dihedral angle formed by four atoms, over a list of coordinates.</span>
 
@@ -637,6 +635,8 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
 <span class="sd">    .. versionadded:: 0.8</span>
 <span class="sd">    .. versionchanged:: 0.9.0</span>
 <span class="sd">       Added optional box argument to account for periodic boundaries in calculation</span>
+<span class="sd">    .. versionchanged:: 0.11.0</span>
+<span class="sd">       Renamed from calc_torsions to calc_dihedrals</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">atom1</span> <span class="o">=</span> <span class="n">coords1</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="s">&#39;C&#39;</span><span class="p">)</span>
     <span class="n">atom2</span> <span class="o">=</span> <span class="n">coords2</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="s">&#39;C&#39;</span><span class="p">)</span>
@@ -674,12 +674,15 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
         <span class="n">calc_dihedral</span><span class="p">(</span><span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">,</span> <span class="n">atom3</span><span class="p">,</span> <span class="n">atom4</span><span class="p">,</span> <span class="n">angles</span><span class="p">)</span>
 
     <span class="k">return</span> <span class="n">angles</span>
-
 </div>
-<div class="viewcode-block" id="applyPBC"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.lib.distances.applyPBC">[docs]</a><span class="k">def</span> <span class="nf">applyPBC</span><span class="p">(</span><span class="n">incoords</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
+<span class="n">calc_torsions</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">calc_dihedrals</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;calc_torsions&#39;</span><span class="p">,</span>
+                          <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;calc_dihedrals&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="apply_PBC"><a class="viewcode-back" href="../../../documentation_pages/lib/distances.html#MDAnalysis.analysis.distances.apply_PBC">[docs]</a><span class="k">def</span> <span class="nf">apply_PBC</span><span class="p">(</span><span class="n">incoords</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Moves a set of coordinates to all be within the primary unit cell</span>
 
-<span class="sd">    newcoords = applyPBC(coords, box)</span>
+<span class="sd">    newcoords = apply_PBC(coords, box)</span>
 
 <span class="sd">    :Arguments:</span>
 <span class="sd">        *coords*</span>
@@ -723,7 +726,9 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
         <span class="n">box_inv</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">/</span> <span class="n">box</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span>
         <span class="n">triclinic_pbc</span><span class="p">(</span><span class="n">coords</span><span class="p">,</span> <span class="n">box</span><span class="p">,</span> <span class="n">box_inv</span><span class="p">)</span>
 
-    <span class="k">return</span> <span class="n">coords</span></div>
+    <span class="k">return</span> <span class="n">coords</span>
+</div>
+<span class="n">applyPBC</span> <span class="o">=</span> <span class="n">deprecate</span><span class="p">(</span><span class="n">apply_PBC</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="s">&#39;applyPBC&#39;</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="s">&#39;apply_PBC&#39;</span><span class="p">)</span>
 </pre></div>
 
           </div>
@@ -731,7 +736,7 @@ <h1>Source code for MDAnalysis.lib.distances</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -740,12 +745,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -755,7 +759,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/lib/log.html b/package/doc/html/_modules/MDAnalysis/lib/log.html
index 79c8c92643c..e95db7e269d 100644
--- a/package/doc/html/_modules/MDAnalysis/lib/log.html
+++ b/package/doc/html/_modules/MDAnalysis/lib/log.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.lib.log &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.lib.log &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.lib.log</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -155,7 +152,7 @@ <h1>Source code for MDAnalysis.lib.log</h1><div class="highlight"><pre>
 
 <span class="kn">from</span> <span class="nn">..</span> <span class="kn">import</span> <span class="n">version</span>
 
-<div class="viewcode-block" id="start_logging"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.lib.log.start_logging">[docs]</a><span class="k">def</span> <span class="nf">start_logging</span><span class="p">(</span><span class="n">logfile</span><span class="o">=</span><span class="s">&quot;MDAnalysis.log&quot;</span><span class="p">,</span> <span class="n">version</span><span class="o">=</span><span class="n">version</span><span class="o">.</span><span class="n">__version__</span><span class="p">):</span>
+<div class="viewcode-block" id="start_logging"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.start_logging">[docs]</a><span class="k">def</span> <span class="nf">start_logging</span><span class="p">(</span><span class="n">logfile</span><span class="o">=</span><span class="s">&quot;MDAnalysis.log&quot;</span><span class="p">,</span> <span class="n">version</span><span class="o">=</span><span class="n">version</span><span class="o">.</span><span class="n">__version__</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Start logging of messages to file and console.</span>
 
 <span class="sd">    The default logfile is named `MDAnalysis.log` and messages are</span>
@@ -166,7 +163,7 @@ <h1>Source code for MDAnalysis.lib.log</h1><div class="highlight"><pre>
         <span class="s">&quot;MDAnalysis </span><span class="si">%s</span><span class="s"> STARTED logging to </span><span class="si">%r</span><span class="s">&quot;</span><span class="p">,</span> <span class="n">version</span><span class="p">,</span> <span class="n">logfile</span><span class="p">)</span>
 
 </div>
-<div class="viewcode-block" id="stop_logging"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.lib.log.stop_logging">[docs]</a><span class="k">def</span> <span class="nf">stop_logging</span><span class="p">():</span>
+<div class="viewcode-block" id="stop_logging"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.stop_logging">[docs]</a><span class="k">def</span> <span class="nf">stop_logging</span><span class="p">():</span>
     <span class="sd">&quot;&quot;&quot;Stop logging to logfile and console.&quot;&quot;&quot;</span>
     <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s">&quot;MDAnalysis&quot;</span><span class="p">)</span>
     <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">&quot;MDAnalysis STOPPED logging&quot;</span><span class="p">)</span>
@@ -174,7 +171,7 @@ <h1>Source code for MDAnalysis.lib.log</h1><div class="highlight"><pre>
 
 
 </div>
-<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.lib.log.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">logger_name</span><span class="o">=</span><span class="s">&quot;MDAnalysis&quot;</span><span class="p">,</span> <span class="n">logfile</span><span class="o">=</span><span class="s">&quot;MDAnalysis.log&quot;</span><span class="p">):</span>
+<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">logger_name</span><span class="o">=</span><span class="s">&quot;MDAnalysis&quot;</span><span class="p">,</span> <span class="n">logfile</span><span class="o">=</span><span class="s">&quot;MDAnalysis.log&quot;</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Create a top level logger.</span>
 
 <span class="sd">    - The file logger logs everything (including DEBUG).</span>
@@ -213,7 +210,7 @@ <h1>Source code for MDAnalysis.lib.log</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">logger</span>
 
 </div>
-<div class="viewcode-block" id="clear_handlers"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.lib.log.clear_handlers">[docs]</a><span class="k">def</span> <span class="nf">clear_handlers</span><span class="p">(</span><span class="n">logger</span><span class="p">):</span>
+<div class="viewcode-block" id="clear_handlers"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.clear_handlers">[docs]</a><span class="k">def</span> <span class="nf">clear_handlers</span><span class="p">(</span><span class="n">logger</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;clean out handlers in the library top level logger</span>
 
 <span class="sd">    (only important for reload/debug cycles...)</span>
@@ -223,7 +220,7 @@ <h1>Source code for MDAnalysis.lib.log</h1><div class="highlight"><pre>
         <span class="n">logger</span><span class="o">.</span><span class="n">removeHandler</span><span class="p">(</span><span class="n">h</span><span class="p">)</span>
 
 </div>
-<div class="viewcode-block" id="NullHandler"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.lib.log.NullHandler">[docs]</a><span class="k">class</span> <span class="nc">NullHandler</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">Handler</span><span class="p">):</span>
+<div class="viewcode-block" id="NullHandler"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.NullHandler">[docs]</a><span class="k">class</span> <span class="nc">NullHandler</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">Handler</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Silent Handler.</span>
 
 <span class="sd">    Useful as a default::</span>
@@ -239,13 +236,13 @@ <h1>Source code for MDAnalysis.lib.log</h1><div class="highlight"><pre>
         <span class="k">pass</span>
 
 </div>
-<div class="viewcode-block" id="echo"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.lib.log.echo">[docs]</a><span class="k">def</span> <span class="nf">echo</span><span class="p">(</span><span class="n">s</span><span class="o">=</span><span class="s">&#39;&#39;</span><span class="p">):</span>
+<div class="viewcode-block" id="echo"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.echo">[docs]</a><span class="k">def</span> <span class="nf">echo</span><span class="p">(</span><span class="n">s</span><span class="o">=</span><span class="s">&#39;&#39;</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Simple string output that immediately prints to the console.&quot;&quot;&quot;</span>
     <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
     <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
 
 </div>
-<div class="viewcode-block" id="ProgressMeter"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.lib.log.ProgressMeter">[docs]</a><span class="k">class</span> <span class="nc">ProgressMeter</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="ProgressMeter"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.ProgressMeter">[docs]</a><span class="k">class</span> <span class="nc">ProgressMeter</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Simple progress meter</span>
 
 <span class="sd">    Usage::</span>
@@ -337,7 +334,7 @@ <h1>Source code for MDAnalysis.lib.log</h1><div class="highlight"><pre>
         <span class="k">assert</span> <span class="n">numsteps</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">,</span> <span class="s">&quot;numsteps step must be &gt;0&quot;</span>
         <span class="k">assert</span> <span class="n">interval</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">,</span> <span class="s">&quot;interval step must be &gt;0&quot;</span>
 
-<div class="viewcode-block" id="ProgressMeter.update"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.lib.log.ProgressMeter.update">[docs]</a>    <span class="k">def</span> <span class="nf">update</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">step</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="ProgressMeter.update"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.ProgressMeter.update">[docs]</a>    <span class="k">def</span> <span class="nf">update</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">step</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Update the state of the ProgressMeter.</span>
 
 <span class="sd">        *kwargs* are additional attributes that can be references in</span>
@@ -350,7 +347,7 @@ <h1>Source code for MDAnalysis.lib.log</h1><div class="highlight"><pre>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">numouts</span> <span class="o">+=</span> <span class="mi">1</span>
 </div>
-<div class="viewcode-block" id="ProgressMeter.echo"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.lib.log.ProgressMeter.echo">[docs]</a>    <span class="k">def</span> <span class="nf">echo</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">step</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="ProgressMeter.echo"><a class="viewcode-back" href="../../../documentation_pages/lib/log.html#MDAnalysis.ProgressMeter.echo">[docs]</a>    <span class="k">def</span> <span class="nf">echo</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">step</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Print the state to stderr, but only every *interval* steps.</span>
 
 <span class="sd">        1) calls :meth:`~ProgressMeter.update`</span>
@@ -387,7 +384,7 @@ <h1>Source code for MDAnalysis.lib.log</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -396,12 +393,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -411,7 +407,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/lib/mdamath.html b/package/doc/html/_modules/MDAnalysis/lib/mdamath.html
index b6bc156ac76..aa6e86c935d 100644
--- a/package/doc/html/_modules/MDAnalysis/lib/mdamath.html
+++ b/package/doc/html/_modules/MDAnalysis/lib/mdamath.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.lib.mdamath &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.lib.mdamath &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.lib.mdamath</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -475,7 +472,7 @@ <h1>Source code for MDAnalysis.lib.mdamath</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -484,12 +481,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -499,7 +495,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/lib/transformations.html b/package/doc/html/_modules/MDAnalysis/lib/transformations.html
index b407a084d9f..56fd8d25eb7 100644
--- a/package/doc/html/_modules/MDAnalysis/lib/transformations.html
+++ b/package/doc/html/_modules/MDAnalysis/lib/transformations.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.lib.transformations &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.lib.transformations &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.lib.transformations</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-</span>
@@ -1919,7 +1916,7 @@ <h1>Source code for MDAnalysis.lib.transformations</h1><div class="highlight"><p
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1928,12 +1925,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1943,7 +1939,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/lib/util.html b/package/doc/html/_modules/MDAnalysis/lib/util.html
index 31e77165a58..4f81467aa60 100644
--- a/package/doc/html/_modules/MDAnalysis/lib/util.html
+++ b/package/doc/html/_modules/MDAnalysis/lib/util.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.lib.util &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.lib.util &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.lib.util</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -110,6 +107,7 @@ <h1>Source code for MDAnalysis.lib.util</h1><div class="highlight"><pre>
 <span class="sd">.. autofunction:: greedy_splitext</span>
 <span class="sd">.. autofunction:: which</span>
 <span class="sd">.. autofunction:: realpath</span>
+<span class="sd">.. autofunction:: guess_format</span>
 
 <span class="sd">Streams</span>
 <span class="sd">-------</span>
@@ -238,6 +236,8 @@ <h1>Source code for MDAnalysis.lib.util</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">functools</span> <span class="kn">import</span> <span class="n">wraps</span>
 <span class="kn">import</span> <span class="nn">numpy</span>
 
+<span class="kn">from</span> <span class="nn">..exceptions</span> <span class="kn">import</span> <span class="n">StreamWarning</span>
+
 
 <span class="c"># Python 3.0, 3.1 do not have the builtin callable()</span>
 <span class="k">try</span><span class="p">:</span>
@@ -355,8 +355,6 @@ <h1>Source code for MDAnalysis.lib.util</h1><div class="highlight"><pre>
 <span class="sd">       Only returns the ``stream`` and tries to set ``stream.name = filename`` instead of the previous</span>
 <span class="sd">       behavior to return a tuple ``(stream, filename)``.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">from</span> <span class="nn">MDAnalysis</span> <span class="kn">import</span> <span class="n">StreamWarning</span>
-
     <span class="n">handlers</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;bz2&#39;</span><span class="p">:</span> <span class="n">bz2</span><span class="o">.</span><span class="n">BZ2File</span><span class="p">,</span> <span class="s">&#39;gz&#39;</span><span class="p">:</span> <span class="n">gzip</span><span class="o">.</span><span class="n">open</span><span class="p">,</span> <span class="s">&#39;&#39;</span><span class="p">:</span> <span class="nb">file</span><span class="p">}</span>
 
     <span class="k">if</span> <span class="n">mode</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">&#39;r&#39;</span><span class="p">):</span>
@@ -607,8 +605,6 @@ <h1>Source code for MDAnalysis.lib.util</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="NamedStream.reset"><a class="viewcode-back" href="../../../documentation_pages/lib/util.html#MDAnalysis.lib.util.NamedStream.reset">[docs]</a>    <span class="k">def</span> <span class="nf">reset</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Move to the beginning of the stream&quot;&quot;&quot;</span>
         <span class="c"># try to rewind</span>
-        <span class="kn">from</span> <span class="nn">MDAnalysis</span> <span class="kn">import</span> <span class="n">StreamWarning</span>
-
         <span class="k">try</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">stream</span><span class="o">.</span><span class="n">reset</span><span class="p">()</span>  <span class="c"># e.g. StreamIO</span>
         <span class="k">except</span> <span class="p">(</span><span class="ne">AttributeError</span><span class="p">,</span> <span class="ne">IOError</span><span class="p">):</span>
@@ -672,13 +668,13 @@ <h1>Source code for MDAnalysis.lib.util</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">close</span><span class="p">(</span><span class="n">force</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
 
     <span class="nd">@property</span>
-<div class="viewcode-block" id="NamedStream.closed"><a class="viewcode-back" href="../../../documentation_pages/lib/util.html#MDAnalysis.lib.util.NamedStream.closed">[docs]</a>    <span class="k">def</span> <span class="nf">closed</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">closed</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;``True`` if stream is closed.&quot;&quot;&quot;</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">stream</span><span class="o">.</span><span class="n">closed</span>
         <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
             <span class="k">return</span> <span class="nb">super</span><span class="p">(</span><span class="n">NamedStream</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">closed</span>
-</div>
+
 <div class="viewcode-block" id="NamedStream.seek"><a class="viewcode-back" href="../../../documentation_pages/lib/util.html#MDAnalysis.lib.util.NamedStream.seek">[docs]</a>    <span class="k">def</span> <span class="nf">seek</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">offset</span><span class="p">,</span> <span class="n">whence</span><span class="o">=</span><span class="n">os</span><span class="o">.</span><span class="n">SEEK_SET</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Change the stream position to the given byte *offset* .</span>
 
@@ -817,6 +813,78 @@ <h1>Source code for MDAnalysis.lib.util</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">None</span>
     <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">realpath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expanduser</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expandvars</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">))))</span>
 
+</div>
+<span class="k">def</span> <span class="nf">get_ext</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;Return the lower-cased extension of *filename* without a leading dot.</span>
+
+<span class="sd">    :Returns: root, ext</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">root</span><span class="p">,</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+    <span class="k">if</span> <span class="n">ext</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">extsep</span><span class="p">):</span>
+        <span class="n">ext</span> <span class="o">=</span> <span class="n">ext</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
+    <span class="k">return</span> <span class="n">root</span><span class="p">,</span> <span class="n">ext</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+
+<span class="k">def</span> <span class="nf">check_compressed_format</span><span class="p">(</span><span class="n">root</span><span class="p">,</span> <span class="n">ext</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;Check if this is a supported gzipped/bzip2ed file format and return UPPERCASE format.&quot;&quot;&quot;</span>
+    <span class="c"># XYZReader&amp;others are setup to handle both plain and compressed (bzip2, gz) files</span>
+    <span class="c"># ..so if the first file extension is bzip2 or gz, look at the one to the left of it</span>
+    <span class="k">if</span> <span class="n">ext</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&quot;bz2&quot;</span><span class="p">,</span> <span class="s">&quot;gz&quot;</span><span class="p">):</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">root</span><span class="p">,</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">get_ext</span><span class="p">(</span><span class="n">root</span><span class="p">)</span>
+        <span class="k">except</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">&quot;Cannot determine coordinate format for &#39;{0}.{1}&#39;&quot;</span>
+                            <span class="s">&quot;&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">root</span><span class="p">,</span> <span class="n">ext</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">ext</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+
+
+<span class="k">def</span> <span class="nf">format_from_filename_extension</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;Guess file format from the file extension&quot;&quot;&quot;</span>
+    <span class="k">try</span><span class="p">:</span>
+        <span class="n">root</span><span class="p">,</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">get_ext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+    <span class="k">except</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span>
+            <span class="s">&quot;Cannot determine file format for file &#39;{0}&#39;.</span><span class="se">\n</span><span class="s">&quot;</span>
+            <span class="s">&quot;           You can set the format explicitly with &quot;</span>
+            <span class="s">&quot;&#39;Universe(..., format=FORMAT)&#39;.&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
+    <span class="n">format</span> <span class="o">=</span> <span class="n">check_compressed_format</span><span class="p">(</span><span class="n">root</span><span class="p">,</span> <span class="n">ext</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">format</span>
+
+
+<div class="viewcode-block" id="guess_format"><a class="viewcode-back" href="../../../documentation_pages/lib/util.html#MDAnalysis.lib.util.guess_format">[docs]</a><span class="k">def</span> <span class="nf">guess_format</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;Return the format of *filename*</span>
+
+<span class="sd">    The current heuristic simply looks at the filename extension</span>
+<span class="sd">    and can work around compressed format extensions</span>
+
+<span class="sd">    *filename* can also be a stream, in which case</span>
+<span class="sd">    *filename.name* is looked at for a hint to the format</span>
+
+<span class="sd">    :Raises:</span>
+<span class="sd">       *ValueError*</span>
+
+<span class="sd">    .. versionadded:: 0.11.0</span>
+<span class="sd">       Moved into lib.util</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="n">isstream</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
+        <span class="c"># perhaps StringIO or open stream</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">format</span> <span class="o">=</span> <span class="n">format_from_filename_extension</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+        <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
+            <span class="c"># format is None so we need to complain:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">&quot;guess_format requires an explicit format specifier &quot;</span>
+                             <span class="s">&quot;for stream {0}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="c"># iterator, list, filename: simple extension checking... something more</span>
+        <span class="c"># complicated is left for the ambitious.</span>
+        <span class="c"># Note: at the moment the upper-case extension *is* the format specifier</span>
+        <span class="c"># and list of filenames is handled by ChainReader</span>
+        <span class="n">format</span> <span class="o">=</span> <span class="p">(</span><span class="n">format_from_filename_extension</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+                  <span class="k">if</span> <span class="ow">not</span> <span class="n">iterable</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span> <span class="k">else</span> <span class="s">&#39;CHAIN&#39;</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">format</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+
 </div>
 <div class="viewcode-block" id="iterable"><a class="viewcode-back" href="../../../documentation_pages/lib/util.html#MDAnalysis.lib.util.iterable">[docs]</a><span class="k">def</span> <span class="nf">iterable</span><span class="p">(</span><span class="n">obj</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Returns ``True`` if *obj* can be iterated over and is *not* a  string.&quot;&quot;&quot;</span>
@@ -1177,7 +1245,7 @@ <h1>Source code for MDAnalysis.lib.util</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1186,12 +1254,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1201,7 +1268,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/selections/base.html b/package/doc/html/_modules/MDAnalysis/selections/base.html
index 24733f924f6..864e2944e40 100644
--- a/package/doc/html/_modules/MDAnalysis/selections/base.html
+++ b/package/doc/html/_modules/MDAnalysis/selections/base.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.selections.base &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.selections.base &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.selections.base</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -191,7 +188,7 @@ <h1>Source code for MDAnalysis.selections.base</h1><div class="highlight"><pre>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">write_preamble</span><span class="p">()</span>
 </div>
-<div class="viewcode-block" id="SelectionWriter.comment"><a class="viewcode-back" href="../../../documentation_pages/selections/base.html#MDAnalysis.selections.base.SelectionWriter.comment">[docs]</a>    <span class="k">def</span> <span class="nf">comment</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">s</span><span class="p">):</span>
+<div class="viewcode-block" id="SelectionWriter.comment"><a class="viewcode-back" href="../../../documentation_pages/selections/vmd.html#MDAnalysis.selections.base.SelectionWriter.comment">[docs]</a>    <span class="k">def</span> <span class="nf">comment</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">s</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Return string *s* interpolated into the comment format string.</span>
 
 <span class="sd">        If no :attr:`SelectionWriter.commentfmt` is defined (None) then the</span>
@@ -204,15 +201,15 @@ <h1>Source code for MDAnalysis.selections.base</h1><div class="highlight"><pre>
             <span class="k">return</span> <span class="s">&#39;&#39;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">commentfmt</span> <span class="o">%</span> <span class="n">s</span> <span class="o">+</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">&#39;</span>
 </div>
-    <span class="k">def</span> <span class="nf">write_preamble</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="SelectionWriter.write_preamble"><a class="viewcode-back" href="../../../documentation_pages/selections/vmd.html#MDAnalysis.selections.base.SelectionWriter.write_preamble">[docs]</a>    <span class="k">def</span> <span class="nf">write_preamble</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Write a header, depending on the file format.&quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">preamble</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
             <span class="k">return</span>
         <span class="k">with</span> <span class="n">util</span><span class="o">.</span><span class="n">openany</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_current_mode</span><span class="p">)</span> <span class="k">as</span> <span class="n">out</span><span class="p">:</span>
             <span class="n">out</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">comment</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">preamble</span><span class="p">))</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_current_mode</span> <span class="o">=</span> <span class="s">&#39;a&#39;</span>
-
-<div class="viewcode-block" id="SelectionWriter.write"><a class="viewcode-back" href="../../../documentation_pages/selections/base.html#MDAnalysis.selections.base.SelectionWriter.write">[docs]</a>    <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">selection</span><span class="p">,</span> <span class="n">number</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">frame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+</div>
+<div class="viewcode-block" id="SelectionWriter.write"><a class="viewcode-back" href="../../../documentation_pages/selections/vmd.html#MDAnalysis.selections.base.SelectionWriter.write">[docs]</a>    <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">selection</span><span class="p">,</span> <span class="n">number</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">frame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Write selection to the output file.</span>
 
 <span class="sd">        :Arguments:</span>
@@ -292,7 +289,7 @@ <h1>Source code for MDAnalysis.selections.base</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -301,12 +298,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -316,7 +312,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/selections/charmm.html b/package/doc/html/_modules/MDAnalysis/selections/charmm.html
index ad3e1e72372..a3a1e40c284 100644
--- a/package/doc/html/_modules/MDAnalysis/selections/charmm.html
+++ b/package/doc/html/_modules/MDAnalysis/selections/charmm.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.selections.charmm &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.selections.charmm &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.selections.charmm</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -140,7 +137,7 @@ <h1>Source code for MDAnalysis.selections.charmm</h1><div class="highlight"><pre
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -149,12 +146,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -164,7 +160,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/selections/gromacs.html b/package/doc/html/_modules/MDAnalysis/selections/gromacs.html
index 1f871e87956..4f7604e5ac5 100644
--- a/package/doc/html/_modules/MDAnalysis/selections/gromacs.html
+++ b/package/doc/html/_modules/MDAnalysis/selections/gromacs.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.selections.gromacs &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.selections.gromacs &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.selections.gromacs</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -131,7 +128,7 @@ <h1>Source code for MDAnalysis.selections.gromacs</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -140,12 +137,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -155,7 +151,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/selections/jmol.html b/package/doc/html/_modules/MDAnalysis/selections/jmol.html
index d6c25b885a3..32aff33bfd4 100644
--- a/package/doc/html/_modules/MDAnalysis/selections/jmol.html
+++ b/package/doc/html/_modules/MDAnalysis/selections/jmol.html
@@ -1,5 +1,3 @@
-
-
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   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.selections.jmol &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.selections.jmol &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.selections.jmol</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -138,7 +135,7 @@ <h1>Source code for MDAnalysis.selections.jmol</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -147,12 +144,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -162,7 +158,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/selections/pymol.html b/package/doc/html/_modules/MDAnalysis/selections/pymol.html
index 13aad9a2865..d9de3d767a3 100644
--- a/package/doc/html/_modules/MDAnalysis/selections/pymol.html
+++ b/package/doc/html/_modules/MDAnalysis/selections/pymol.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.selections.pymol &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.selections.pymol &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.selections.pymol</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -138,7 +135,7 @@ <h1>Source code for MDAnalysis.selections.pymol</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -147,12 +144,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -162,7 +158,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/selections/vmd.html b/package/doc/html/_modules/MDAnalysis/selections/vmd.html
index 6e8856aacd0..8c0eae18d8f 100644
--- a/package/doc/html/_modules/MDAnalysis/selections/vmd.html
+++ b/package/doc/html/_modules/MDAnalysis/selections/vmd.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.selections.vmd &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.selections.vmd &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.selections.vmd</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -135,7 +132,7 @@ <h1>Source code for MDAnalysis.selections.vmd</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -144,12 +141,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -159,7 +155,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/CRDParser.html b/package/doc/html/_modules/MDAnalysis/topology/CRDParser.html
index 6bbd131972b..cb902b267fb 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/CRDParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/CRDParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.CRDParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.CRDParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.CRDParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -168,7 +165,7 @@ <h1>Source code for MDAnalysis.topology.CRDParser</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
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         <li class="right" style="margin-right: 10px">
@@ -177,12 +174,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -192,7 +188,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/DMSParser.html b/package/doc/html/_modules/MDAnalysis/topology/DMSParser.html
index 6d9d8257d9e..4849bf43206 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/DMSParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/DMSParser.html
@@ -1,5 +1,3 @@
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-
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@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.DMSParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.DMSParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
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       var DOCUMENTATION_OPTIONS = {
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-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
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     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.DMSParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -203,7 +200,7 @@ <h1>Source code for MDAnalysis.topology.DMSParser</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -212,12 +209,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -227,7 +223,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/ExtendedPDBParser.html b/package/doc/html/_modules/MDAnalysis/topology/ExtendedPDBParser.html
index ca0509f60b3..7de918a3413 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/ExtendedPDBParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/ExtendedPDBParser.html
@@ -1,5 +1,3 @@
-
-
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@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.ExtendedPDBParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.ExtendedPDBParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.ExtendedPDBParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -150,7 +147,7 @@ <h1>Source code for MDAnalysis.topology.ExtendedPDBParser</h1><div class="highli
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -159,12 +156,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -174,7 +170,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/GMSParser.html b/package/doc/html/_modules/MDAnalysis/topology/GMSParser.html
index 4721d2b7cdb..6680d415d30 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/GMSParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/GMSParser.html
@@ -1,5 +1,3 @@
-
-
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@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.GMSParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.GMSParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.GMSParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -174,7 +171,7 @@ <h1>Source code for MDAnalysis.topology.GMSParser</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -183,12 +180,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -198,7 +194,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/GROParser.html b/package/doc/html/_modules/MDAnalysis/topology/GROParser.html
index d30b244b583..0254f3f643e 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/GROParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/GROParser.html
@@ -1,5 +1,3 @@
-
-
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@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.GROParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.GROParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
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     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.GROParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -180,7 +177,7 @@ <h1>Source code for MDAnalysis.topology.GROParser</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -189,12 +186,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -204,7 +200,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/HoomdXMLParser.html b/package/doc/html/_modules/MDAnalysis/topology/HoomdXMLParser.html
index bdec1ecb802..2a919383fda 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/HoomdXMLParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/HoomdXMLParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.HoomdXMLParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.HoomdXMLParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.HoomdXMLParser</h1><div class="highlight"><pre>
 <span class="c"># MDAnalysis --- http://www.MDAnalysis.org</span>
@@ -89,7 +86,10 @@ <h1>Source code for MDAnalysis.topology.HoomdXMLParser</h1><div class="highlight
 
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">HOOMD XML topology parser</span>
-<span class="sd">========================</span>
+<span class="sd">=========================</span>
+
+<span class="sd">.. versionadded:: 0.11.0</span>
+
 <span class="sd">The :class:`HoomdXMLParser` generates a topology from files for the HOOMD_ code.</span>
 
 <span class="sd">Read a list of atoms from a `HOOMD XML`_ file to build a basic topology.</span>
@@ -109,6 +109,7 @@ <h1>Source code for MDAnalysis.topology.HoomdXMLParser</h1><div class="highlight
 <span class="sd">.. autoclass:: HoomdXMLParser</span>
 <span class="sd">   :members:</span>
 <span class="sd">   :inherited-members:</span>
+
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">absolute_import</span>
 <span class="kn">from</span> <span class="nn">..lib.util</span> <span class="kn">import</span> <span class="n">openany</span>
@@ -120,7 +121,7 @@ <h1>Source code for MDAnalysis.topology.HoomdXMLParser</h1><div class="highlight
 <div class="viewcode-block" id="HoomdXMLParser"><a class="viewcode-back" href="../../../documentation_pages/topology/HoomdXMLParser.html#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser">[docs]</a><span class="k">class</span> <span class="nc">HoomdXMLParser</span><span class="p">(</span><span class="n">TopologyReader</span><span class="p">):</span>
 <div class="viewcode-block" id="HoomdXMLParser.parse"><a class="viewcode-back" href="../../../documentation_pages/topology/HoomdXMLParser.html#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.parse">[docs]</a>    <span class="k">def</span> <span class="nf">parse</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Parse Hoomd XML file *filename* and return the dict `structure`.</span>
-<span class="sd">            </span>
+
 <span class="sd">           Hoomd XML format does not contain a node for names. The parser will</span>
 <span class="sd">           look for a name node anyway, and if it doesn&#39;t find one, it will use</span>
 <span class="sd">           the atom types as names. If the Hoomd XML file doesn&#39;t contain a type</span>
@@ -134,7 +135,9 @@ <h1>Source code for MDAnalysis.topology.HoomdXMLParser</h1><div class="highlight
 <span class="sd">           :Returns: MDAnalysis internal *structure* dict</span>
 
 <span class="sd">           .. SeeAlso:: The *structure* dict is defined in</span>
-<span class="sd">           :func:`MDAnalysis.topology.base`.</span>
+<span class="sd">                        :func:`MDAnalysis.topology.base`.</span>
+
+<span class="sd">           .. versionadded:: 0.11.0</span>
 
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">with</span> <span class="n">openany</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">)</span> <span class="k">as</span> <span class="n">stream</span><span class="p">:</span>
@@ -244,7 +247,7 @@ <h1>Source code for MDAnalysis.topology.HoomdXMLParser</h1><div class="highlight
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -253,12 +256,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -268,7 +270,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/LAMMPSParser.html b/package/doc/html/_modules/MDAnalysis/topology/LAMMPSParser.html
index 4b14d0845dc..67b15d4565c 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/LAMMPSParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/LAMMPSParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.LAMMPSParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.LAMMPSParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.LAMMPSParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -671,7 +668,7 @@ <h1>Source code for MDAnalysis.topology.LAMMPSParser</h1><div class="highlight">
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -680,12 +677,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -695,7 +691,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/MOL2Parser.html b/package/doc/html/_modules/MDAnalysis/topology/MOL2Parser.html
index 19f313cc970..1b45d92ff71 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/MOL2Parser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/MOL2Parser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.MOL2Parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.MOL2Parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.MOL2Parser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -212,7 +209,7 @@ <h1>Source code for MDAnalysis.topology.MOL2Parser</h1><div class="highlight"><p
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -221,12 +218,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -236,7 +232,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/PDBParser.html b/package/doc/html/_modules/MDAnalysis/topology/PDBParser.html
index f268ee29c3e..a0241655caa 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/PDBParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/PDBParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.PDBParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.PDBParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
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-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.PDBParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -179,7 +176,7 @@ <h1>Source code for MDAnalysis.topology.PDBParser</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -188,12 +185,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -203,7 +199,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/PDBQTParser.html b/package/doc/html/_modules/MDAnalysis/topology/PDBQTParser.html
index 193596bdeb7..d88a1012ffe 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/PDBQTParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/PDBQTParser.html
@@ -1,5 +1,3 @@
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@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.PDBQTParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.PDBQTParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.PDBQTParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -172,7 +169,7 @@ <h1>Source code for MDAnalysis.topology.PDBQTParser</h1><div class="highlight"><
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -181,12 +178,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -196,7 +192,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/PQRParser.html b/package/doc/html/_modules/MDAnalysis/topology/PQRParser.html
index 087ae7c7731..437dfb27cb8 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/PQRParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/PQRParser.html
@@ -1,5 +1,3 @@
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-
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   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.PQRParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.PQRParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.PQRParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -175,7 +172,7 @@ <h1>Source code for MDAnalysis.topology.PQRParser</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -184,12 +181,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -199,7 +195,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/PSFParser.html b/package/doc/html/_modules/MDAnalysis/topology/PSFParser.html
index bd3d8369223..0016baa0e97 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/PSFParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/PSFParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.PSFParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.PSFParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.PSFParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -323,7 +320,7 @@ <h1>Source code for MDAnalysis.topology.PSFParser</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -332,12 +329,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -347,7 +343,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/PrimitivePDBParser.html b/package/doc/html/_modules/MDAnalysis/topology/PrimitivePDBParser.html
index 2f7b9e7f1a2..bf7663d7327 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/PrimitivePDBParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/PrimitivePDBParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.PrimitivePDBParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.PrimitivePDBParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.PrimitivePDBParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -131,7 +128,7 @@ <h1>Source code for MDAnalysis.topology.PrimitivePDBParser</h1><div class="highl
 <span class="kn">from</span> <span class="nn">.base</span> <span class="kn">import</span> <span class="n">TopologyReader</span>
 
 
-<div class="viewcode-block" id="PrimitivePDBParser"><a class="viewcode-back" href="../../../documentation_pages/topology/PrimitivePDBParser.html#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser">[docs]</a><span class="k">class</span> <span class="nc">PrimitivePDBParser</span><span class="p">(</span><span class="n">TopologyReader</span><span class="p">):</span>
+<div class="viewcode-block" id="PrimitivePDBParser"><a class="viewcode-back" href="../../../documentation_pages/topology/PrimitivePDBParser.html#MDAnalysis.topology.ExtendedPDBParser.PrimitivePDBParser">[docs]</a><span class="k">class</span> <span class="nc">PrimitivePDBParser</span><span class="p">(</span><span class="n">TopologyReader</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Parser that obtains a list of atoms from a standard PDB file.</span>
 
 <span class="sd">    .. seealso:: :class:`MDAnalysis.coordinates.PDB.PrimitivePDBReader`</span>
@@ -140,7 +137,7 @@ <h1>Source code for MDAnalysis.topology.PrimitivePDBParser</h1><div class="highl
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">format</span> <span class="o">=</span> <span class="s">&#39;PDB&#39;</span>
 
-<div class="viewcode-block" id="PrimitivePDBParser.parse"><a class="viewcode-back" href="../../../documentation_pages/topology/PrimitivePDBParser.html#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.parse">[docs]</a>    <span class="k">def</span> <span class="nf">parse</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="PrimitivePDBParser.parse"><a class="viewcode-back" href="../../../documentation_pages/topology/PrimitivePDBParser.html#MDAnalysis.topology.ExtendedPDBParser.PrimitivePDBParser.parse">[docs]</a>    <span class="k">def</span> <span class="nf">parse</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Parse atom information from PDB file *filename*.</span>
 
 <span class="sd">        :Returns: MDAnalysis internal *structure* dict</span>
@@ -185,7 +182,10 @@ <h1>Source code for MDAnalysis.topology.PrimitivePDBParser</h1><div class="highl
                         <span class="n">resSeq</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">22</span><span class="p">:</span><span class="mi">26</span><span class="p">])</span>
                         <span class="c"># insertCode = _c(27, 27, str)  # not used</span>
                         <span class="c"># occupancy = float(line[54:60])</span>
-                    <span class="n">tempFactor</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">60</span><span class="p">:</span><span class="mi">66</span><span class="p">])</span>
+                    <span class="k">try</span><span class="p">:</span>
+                        <span class="n">tempFactor</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">60</span><span class="p">:</span><span class="mi">66</span><span class="p">])</span>
+                    <span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
+                        <span class="n">tempFactor</span> <span class="o">=</span> <span class="mf">0.0</span>
                     <span class="n">segID</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">66</span><span class="p">:</span><span class="mi">76</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
                     <span class="n">element</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">76</span><span class="p">:</span><span class="mi">78</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
 
@@ -238,7 +238,7 @@ <h1>Source code for MDAnalysis.topology.PrimitivePDBParser</h1><div class="highl
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -247,12 +247,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -262,7 +261,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/TOPParser.html b/package/doc/html/_modules/MDAnalysis/topology/TOPParser.html
index ec9618a3a73..a364d81ef0b 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/TOPParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/TOPParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.TOPParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.TOPParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.TOPParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -355,7 +352,7 @@ <h1>Source code for MDAnalysis.topology.TOPParser</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -364,12 +361,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -379,7 +375,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/TPRParser.html b/package/doc/html/_modules/MDAnalysis/topology/TPRParser.html
index d51ac8cbccc..fddc46e0c0b 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/TPRParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/TPRParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.TPRParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.TPRParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.TPRParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -305,7 +302,7 @@ <h1>Source code for MDAnalysis.topology.TPRParser</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -314,12 +311,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -329,7 +325,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/XYZParser.html b/package/doc/html/_modules/MDAnalysis/topology/XYZParser.html
index b9ecab838ed..e1badaa73be 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/XYZParser.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/XYZParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.XYZParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.XYZParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.XYZParser</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -159,7 +156,7 @@ <h1>Source code for MDAnalysis.topology.XYZParser</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -168,12 +165,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -183,7 +179,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/base.html b/package/doc/html/_modules/MDAnalysis/topology/base.html
index f3c4d77ab7b..9f8929d409b 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/base.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/base.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.base &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.base &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.base</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -154,7 +151,7 @@ <h1>Source code for MDAnalysis.topology.base</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -163,12 +160,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -178,7 +174,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/core.html b/package/doc/html/_modules/MDAnalysis/topology/core.html
index dffd8763e41..19d1eaf546c 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/core.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/core.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.core &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.core &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.core</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -113,6 +110,7 @@ <h1>Source code for MDAnalysis.topology.core</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">tables</span>
 <span class="kn">from</span> <span class="nn">..lib</span> <span class="kn">import</span> <span class="n">distances</span>
 <span class="kn">from</span> <span class="nn">..lib.util</span> <span class="kn">import</span> <span class="n">cached</span>
+<span class="kn">from</span> <span class="nn">..lib</span> <span class="kn">import</span> <span class="n">util</span>
 <span class="kn">from</span> <span class="nn">..core</span> <span class="kn">import</span> <span class="n">AtomGroup</span>
 
 
@@ -127,13 +125,16 @@ <h1>Source code for MDAnalysis.topology.core</h1><div class="highlight"><pre>
 <span class="sd">    :class:`~MDAnalysis.core.AtomGroup.Atom` instances, which record</span>
 <span class="sd">    to which residue and segment an atom belongs.</span>
 
-<span class="sd">    :Returns: structure dict, which associates a segname with a</span>
-<span class="sd">              :class:`~MDAnalysis.core.AtomGroup.Segment`</span>
+<span class="sd">    :Returns: List of :class:`~MDAnalysis.core.AtomGroup.Segment`</span>
+<span class="sd">              instances</span>
 
 <span class="sd">    .. versionchanged:: 0.9.0</span>
 <span class="sd">       Now allows resids in a given :class:`Segment` to be given in non sequential order.</span>
+<span class="sd">    .. versionchanged:: 0.11.0</span>
+<span class="sd">       Returns a list instead of a dict for consistency with the outputs of</span>
+<span class="sd">       :func:`build_residues`</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">struc</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">struc</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
     <span class="n">resatomlist</span> <span class="o">=</span> <span class="n">defaultdict</span><span class="p">(</span><span class="nb">list</span><span class="p">)</span>
     <span class="n">curr_segname</span> <span class="o">=</span> <span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">segid</span>
 
@@ -145,7 +146,7 @@ <h1>Source code for MDAnalysis.topology.core</h1><div class="highlight"><pre>
             <span class="c"># Build the Segment we just left</span>
             <span class="n">residues</span> <span class="o">=</span> <span class="p">[</span><span class="n">AtomGroup</span><span class="o">.</span><span class="n">Residue</span><span class="p">(</span><span class="n">ats</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">resname</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">ats</span><span class="p">)</span>
                         <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">ats</span> <span class="ow">in</span> <span class="n">resatomlist</span><span class="o">.</span><span class="n">iteritems</span><span class="p">()]</span>
-            <span class="n">struc</span><span class="p">[</span><span class="n">curr_segname</span><span class="p">]</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="o">.</span><span class="n">Segment</span><span class="p">(</span><span class="n">curr_segname</span><span class="p">,</span> <span class="n">residues</span><span class="p">)</span>
+            <span class="n">struc</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">AtomGroup</span><span class="o">.</span><span class="n">Segment</span><span class="p">(</span><span class="n">curr_segname</span><span class="p">,</span> <span class="n">residues</span><span class="p">))</span>
 
             <span class="c"># Reset things and start again</span>
             <span class="n">resatomlist</span> <span class="o">=</span> <span class="n">defaultdict</span><span class="p">(</span><span class="nb">list</span><span class="p">)</span>
@@ -155,7 +156,7 @@ <h1>Source code for MDAnalysis.topology.core</h1><div class="highlight"><pre>
     <span class="c"># Add the last segment</span>
     <span class="n">residues</span> <span class="o">=</span> <span class="p">[</span><span class="n">AtomGroup</span><span class="o">.</span><span class="n">Residue</span><span class="p">(</span><span class="n">ats</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">resname</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">ats</span><span class="p">)</span>
                 <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">ats</span> <span class="ow">in</span> <span class="n">resatomlist</span><span class="o">.</span><span class="n">iteritems</span><span class="p">()]</span>
-    <span class="n">struc</span><span class="p">[</span><span class="n">curr_segname</span><span class="p">]</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="o">.</span><span class="n">Segment</span><span class="p">(</span><span class="n">curr_segname</span><span class="p">,</span> <span class="n">residues</span><span class="p">)</span>
+    <span class="n">struc</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">AtomGroup</span><span class="o">.</span><span class="n">Segment</span><span class="p">(</span><span class="n">curr_segname</span><span class="p">,</span> <span class="n">residues</span><span class="p">))</span>
     <span class="k">return</span> <span class="n">struc</span>
 
 </div>
@@ -183,69 +184,37 @@ <h1>Source code for MDAnalysis.topology.core</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">residues</span>
 
 </div>
-<div class="viewcode-block" id="get_parser_for"><a class="viewcode-back" href="../../../documentation_pages/topology/core.html#MDAnalysis.topology.core.get_parser_for">[docs]</a><span class="k">def</span> <span class="nf">get_parser_for</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">permissive</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span> <span class="n">tformat</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+<div class="viewcode-block" id="get_parser_for"><a class="viewcode-back" href="../../../documentation_pages/topology/core.html#MDAnalysis.topology.core.get_parser_for">[docs]</a><span class="k">def</span> <span class="nf">get_parser_for</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">permissive</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Return the appropriate topology parser for *filename*.</span>
 
 <span class="sd">    Automatic detection is disabled when an explicit *format* is</span>
 <span class="sd">    provided.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">_topology_parsers</span>
-
-    <span class="n">tformat</span> <span class="o">=</span> <span class="n">guess_format</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="n">tformat</span><span class="p">)</span>
-    <span class="k">if</span> <span class="n">tformat</span> <span class="o">==</span> <span class="s">&#39;PDB&#39;</span> <span class="ow">and</span> <span class="n">permissive</span><span class="p">:</span>
-        <span class="k">return</span> <span class="n">_topology_parsers</span><span class="p">[</span><span class="s">&#39;Permissive_PDB&#39;</span><span class="p">]</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="k">return</span> <span class="n">_topology_parsers</span><span class="p">[</span><span class="n">tformat</span><span class="p">]</span>
-
-</div>
-<div class="viewcode-block" id="guess_format"><a class="viewcode-back" href="../../../documentation_pages/topology/core.html#MDAnalysis.topology.core.guess_format">[docs]</a><span class="k">def</span> <span class="nf">guess_format</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Returns the type of topology file *filename*.</span>
-
-<span class="sd">    The current heuristic simply looks at the filename extension but</span>
-<span class="sd">    more complicated probes could be implemented here or in the</span>
-<span class="sd">    individual packages (e.g. as static methods).</span>
 
-<span class="sd">    If *format* is supplied then it overrides the auto detection.</span>
+<span class="sd">    :Raises:</span>
+<span class="sd">      *ValueError*</span>
+<span class="sd">        If no appropriate parser could be found.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">_topology_parsers</span>
 
     <span class="k">if</span> <span class="n">format</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="c"># simple extension checking... something more complicated is left</span>
-        <span class="c"># for the ambitious</span>
-        <span class="k">try</span><span class="p">:</span>
-            <span class="n">root</span><span class="p">,</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-            <span class="k">if</span> <span class="n">ext</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">&#39;.&#39;</span><span class="p">):</span>
-                <span class="n">ext</span> <span class="o">=</span> <span class="n">ext</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
-            <span class="n">format</span> <span class="o">=</span> <span class="n">ext</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
-        <span class="k">except</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span>
-                <span class="s">&quot;Cannot autodetect topology type for file &#39;{0}&#39; &quot;</span>
-                <span class="s">&quot;(file extension could not be parsed).</span><span class="se">\n</span><span class="s">&quot;</span>
-                <span class="s">&quot;           You can use &#39;Universe(topology, ..., topology_format=FORMAT)&#39; &quot;</span>
-                <span class="s">&quot;to explicitly specify the format and</span><span class="se">\n</span><span class="s">&quot;</span>
-                <span class="s">&quot;           override automatic detection. Known FORMATs are:</span><span class="se">\n</span><span class="s">&quot;</span>
-                <span class="s">&quot;           {1}</span><span class="se">\n</span><span class="s">&quot;</span>
-                <span class="s">&quot;           See http://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats</span><span class="se">\n</span><span class="s">&quot;</span>
-                <span class="s">&quot;           For missing formats, raise an issue at &quot;</span>
-                <span class="s">&quot;http://issues.mdanalysis.org&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">_topology_parsers</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
-                <span class="c">#TypeError: ....&quot;</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="c"># internally, formats are all uppercase</span>
-        <span class="n">format</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">format</span><span class="p">)</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
-
-    <span class="c"># sanity check</span>
-    <span class="k">if</span> <span class="n">format</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">_topology_parsers</span><span class="p">:</span>
-        <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span>
-            <span class="s">&quot;Unknown topology format &#39;{0}&#39; for file &#39;{1}&#39;.</span><span class="se">\n</span><span class="s">&quot;</span>
-            <span class="s">&quot;           The following FORMATs are implemented in MDAnalysis:</span><span class="se">\n</span><span class="s">&quot;</span>
-            <span class="s">&quot;           {2}</span><span class="se">\n</span><span class="s">&quot;</span>
+        <span class="n">format</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">guess_format</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+    <span class="n">format</span> <span class="o">=</span> <span class="n">format</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+    <span class="k">if</span> <span class="n">format</span> <span class="o">==</span> <span class="s">&#39;PDB&#39;</span> <span class="ow">and</span> <span class="n">permissive</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">_topology_parsers</span><span class="p">[</span><span class="s">&#39;Permissive_PDB&#39;</span><span class="p">]</span>
+
+    <span class="k">try</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">_topology_parsers</span><span class="p">[</span><span class="n">format</span><span class="p">]</span>
+    <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+            <span class="s">&quot;Cannot autodetect topology type for file &#39;{0}&#39; &quot;</span>
+            <span class="s">&quot;(file extension could not be parsed).</span><span class="se">\n</span><span class="s">&quot;</span>
+            <span class="s">&quot;           You can use &#39;Universe(topology, ..., topology_format=FORMAT)&#39; &quot;</span>
+            <span class="s">&quot;to explicitly specify the format and</span><span class="se">\n</span><span class="s">&quot;</span>
+            <span class="s">&quot;           override automatic detection. Known FORMATs are:</span><span class="se">\n</span><span class="s">&quot;</span>
+            <span class="s">&quot;           {1}</span><span class="se">\n</span><span class="s">&quot;</span>
             <span class="s">&quot;           See http://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats</span><span class="se">\n</span><span class="s">&quot;</span>
-            <span class="s">&quot;           You can use &#39;Universe(topology, ..., topology_format=FORMAT)&#39; to explicitly</span><span class="se">\n</span><span class="s">&quot;</span>
-            <span class="s">&quot;           specify the format and override automatic detection.</span><span class="se">\n</span><span class="s">&quot;</span>
             <span class="s">&quot;           For missing formats, raise an issue at &quot;</span>
-            <span class="s">&quot;http://issues.mdanalysis.org&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">format</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">_topology_parsers</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
-            <span class="c">#TypeError: ....&quot;</span>
-    <span class="k">return</span> <span class="n">format</span>
+            <span class="s">&quot;http://issues.mdanalysis.org&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">_topology_parsers</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
 
 
 <span class="c"># following guess_* used by PDB parser</span></div>
@@ -530,7 +499,7 @@ <h1>Source code for MDAnalysis.topology.core</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -539,12 +508,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -554,7 +522,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/tables.html b/package/doc/html/_modules/MDAnalysis/topology/tables.html
index ab003344fb9..96c9697e016 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/tables.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/tables.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.tables &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.tables &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.tables</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -380,7 +377,7 @@ <h1>Source code for MDAnalysis.topology.tables</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -389,12 +386,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -404,7 +400,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/tpr/obj.html b/package/doc/html/_modules/MDAnalysis/topology/tpr/obj.html
index ce5daf9da84..f27a43fc519 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/tpr/obj.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/tpr/obj.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.tpr.obj &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.tpr.obj &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../../index.html" />
-    <link rel="up" title="MDAnalysis.topology.tpr" href="../tpr.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../../index.html" />
+    <link rel="up" title="Module code" href="../../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,18 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li>
-          <li><a href="../tpr.html" accesskey="U">MDAnalysis.topology.tpr</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../../index.html">
               <img class="logo" src="../../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../../search.html" method="get">
       <input type="text" name="q" />
@@ -73,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.tpr.obj</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -212,7 +208,7 @@ <h1>Source code for MDAnalysis.topology.tpr.obj</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -221,13 +217,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li>
-          <li><a href="../tpr.html" >MDAnalysis.topology.tpr</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -237,7 +231,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/topology/tpr/utils.html b/package/doc/html/_modules/MDAnalysis/topology/tpr/utils.html
index 5a43b637cf9..832759403bd 100644
--- a/package/doc/html/_modules/MDAnalysis/topology/tpr/utils.html
+++ b/package/doc/html/_modules/MDAnalysis/topology/tpr/utils.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.topology.tpr.utils &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.topology.tpr.utils &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../../index.html" />
-    <link rel="up" title="MDAnalysis.topology.tpr" href="../tpr.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../../index.html" />
+    <link rel="up" title="Module code" href="../../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,18 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li>
-          <li><a href="../tpr.html" accesskey="U">MDAnalysis.topology.tpr</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../../index.html">
               <img class="logo" src="../../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../../search.html" method="get">
       <input type="text" name="q" />
@@ -73,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.topology.tpr.utils</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -1017,7 +1013,7 @@ <h1>Source code for MDAnalysis.topology.tpr.utils</h1><div class="highlight"><pr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
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         <li class="right" style="margin-right: 10px">
@@ -1026,13 +1022,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li>
-          <li><a href="../tpr.html" >MDAnalysis.topology.tpr</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1042,7 +1036,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/units.html b/package/doc/html/_modules/MDAnalysis/units.html
index 203db155d19..6c89809dfc9 100644
--- a/package/doc/html/_modules/MDAnalysis/units.html
+++ b/package/doc/html/_modules/MDAnalysis/units.html
@@ -1,5 +1,3 @@
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   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.units &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.units &mdash; MDAnalysis 0.11.0 documentation</title>
     
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     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
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-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
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     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
+    <link rel="up" title="Module code" href="../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.units</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -440,7 +437,7 @@ <h1>Source code for MDAnalysis.units</h1><div class="highlight"><pre>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -449,12 +446,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -464,7 +460,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/visualization/streamlines.html b/package/doc/html/_modules/MDAnalysis/visualization/streamlines.html
index 8186f8a0bc6..bdd85a54b36 100644
--- a/package/doc/html/_modules/MDAnalysis/visualization/streamlines.html
+++ b/package/doc/html/_modules/MDAnalysis/visualization/streamlines.html
@@ -1,5 +1,3 @@
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@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.visualization.streamlines &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.visualization.streamlines &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
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+        VERSION:     '0.11.0',
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         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.visualization.streamlines</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -365,7 +362,7 @@ <h1>Source code for MDAnalysis.visualization.streamlines</h1><div class="highlig
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -374,12 +371,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -389,7 +385,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/visualization/streamlines_3D.html b/package/doc/html/_modules/MDAnalysis/visualization/streamlines_3D.html
index f38674a3afb..93c8ff48d6a 100644
--- a/package/doc/html/_modules/MDAnalysis/visualization/streamlines_3D.html
+++ b/package/doc/html/_modules/MDAnalysis/visualization/streamlines_3D.html
@@ -1,5 +1,3 @@
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-
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@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis.visualization.streamlines_3D &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis.visualization.streamlines_3D &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
-    <link rel="up" title="MDAnalysis" href="../../MDAnalysis.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
+    <link rel="up" title="Module code" href="../../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -43,17 +41,16 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" accesskey="U">MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +69,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1>Source code for MDAnalysis.visualization.streamlines_3D</h1><div class="highlight"><pre>
 <span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
@@ -505,7 +502,7 @@ <h1>Source code for MDAnalysis.visualization.streamlines_3D</h1><div class="high
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -514,12 +511,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../index.html" >Module code</a> &raquo;</li>
-          <li><a href="../../MDAnalysis.html" >MDAnalysis</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -529,7 +525,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/_modules/index.html b/package/doc/html/_modules/index.html
index b14f2fa6a23..a343bd6f0c6 100644
--- a/package/doc/html/_modules/index.html
+++ b/package/doc/html/_modules/index.html
@@ -1,5 +1,3 @@
-
-
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@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>Overview: module code &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>Overview: module code &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,13 +25,13 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
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+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
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@@ -69,10 +67,9 @@ <h3>Quick search</h3>
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@@ -98,11 +95,8 @@ <h1>All modules for which code is available</h1>
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 <li><a href="MDAnalysis/coordinates/TRZ.html">MDAnalysis.coordinates.TRZ</a></li>
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@@ -110,19 +104,15 @@ <h1>All modules for which code is available</h1>
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-<li><a href="MDAnalysis/lib/KDTree/NeighborSearch.html">MDAnalysis.lib.KDTree.NeighborSearch</a></li>
+<li><a href="MDAnalysis/lib/NeighborSearch.html">MDAnalysis.lib.NeighborSearch</a></li>
 <li><a href="MDAnalysis/lib/distances.html">MDAnalysis.lib.distances</a></li>
 <li><a href="MDAnalysis/lib/log.html">MDAnalysis.lib.log</a></li>
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@@ -150,22 +140,23 @@ <h1>All modules for which code is available</h1>
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-<li><a href="MDAnalysis/topology/tpr/setting.html">MDAnalysis.topology.tpr.setting</a></li>
+<li><a href="MDAnalysis/topology/tpr/obj.html">MDAnalysis.topology.tpr.obj</a></li>
 <li><a href="MDAnalysis/topology/tpr/utils.html">MDAnalysis.topology.tpr.utils</a></li>
-</ul><li><a href="MDAnalysis/units.html">MDAnalysis.units</a></li>
-<li><a href="MDAnalysis/version.html">MDAnalysis.version</a></li>
+<li><a href="MDAnalysis/units.html">MDAnalysis.units</a></li>
 <li><a href="MDAnalysis/visualization/streamlines.html">MDAnalysis.visualization.streamlines</a></li>
 <li><a href="MDAnalysis/visualization/streamlines_3D.html">MDAnalysis.visualization.streamlines_3D</a></li>
-</ul></ul>
+<li><a href="gridData/core.html">gridData.core</a></li>
+<li><a href="lib/parallel/distances.html">lib.parallel.distances</a></li>
+<li><a href="lib/qcprot.html">lib.qcprot</a></li>
+<li><a href="numpy/lib/utils.html">numpy.lib.utils</a></li>
+</ul>
 
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@@ -174,10 +165,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
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+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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diff --git a/package/doc/html/_modules/numpy/lib/utils.html b/package/doc/html/_modules/numpy/lib/utils.html
new file mode 100644
index 00000000000..e43680a56e3
--- /dev/null
+++ b/package/doc/html/_modules/numpy/lib/utils.html
@@ -0,0 +1,1284 @@
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+            
+  <h1>Source code for numpy.lib.utils</h1><div class="highlight"><pre>
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">division</span><span class="p">,</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">print_function</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">types</span>
+<span class="kn">import</span> <span class="nn">re</span>
+
+<span class="kn">from</span> <span class="nn">numpy.core.numerictypes</span> <span class="kn">import</span> <span class="n">issubclass_</span><span class="p">,</span> <span class="n">issubsctype</span><span class="p">,</span> <span class="n">issubdtype</span>
+<span class="kn">from</span> <span class="nn">numpy.core</span> <span class="kn">import</span> <span class="n">ndarray</span><span class="p">,</span> <span class="n">ufunc</span><span class="p">,</span> <span class="n">asarray</span>
+
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span>
+    <span class="s">&#39;issubclass_&#39;</span><span class="p">,</span> <span class="s">&#39;issubsctype&#39;</span><span class="p">,</span> <span class="s">&#39;issubdtype&#39;</span><span class="p">,</span> <span class="s">&#39;deprecate&#39;</span><span class="p">,</span>
+    <span class="s">&#39;deprecate_with_doc&#39;</span><span class="p">,</span> <span class="s">&#39;get_include&#39;</span><span class="p">,</span> <span class="s">&#39;info&#39;</span><span class="p">,</span> <span class="s">&#39;source&#39;</span><span class="p">,</span> <span class="s">&#39;who&#39;</span><span class="p">,</span>
+    <span class="s">&#39;lookfor&#39;</span><span class="p">,</span> <span class="s">&#39;byte_bounds&#39;</span><span class="p">,</span> <span class="s">&#39;safe_eval&#39;</span>
+    <span class="p">]</span>
+
+<span class="k">def</span> <span class="nf">get_include</span><span class="p">():</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Return the directory that contains the NumPy \\*.h header files.</span>
+
+<span class="sd">    Extension modules that need to compile against NumPy should use this</span>
+<span class="sd">    function to locate the appropriate include directory.</span>
+
+<span class="sd">    Notes</span>
+<span class="sd">    -----</span>
+<span class="sd">    When using ``distutils``, for example in ``setup.py``.</span>
+<span class="sd">    ::</span>
+
+<span class="sd">        import numpy as np</span>
+<span class="sd">        ...</span>
+<span class="sd">        Extension(&#39;extension_name&#39;, ...</span>
+<span class="sd">                include_dirs=[np.get_include()])</span>
+<span class="sd">        ...</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="kn">import</span> <span class="nn">numpy</span>
+    <span class="k">if</span> <span class="n">numpy</span><span class="o">.</span><span class="n">show_config</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+        <span class="c"># running from numpy source directory</span>
+        <span class="n">d</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">__file__</span><span class="p">),</span> <span class="s">&#39;core&#39;</span><span class="p">,</span> <span class="s">&#39;include&#39;</span><span class="p">)</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="c"># using installed numpy core headers</span>
+        <span class="kn">import</span> <span class="nn">numpy.core</span> <span class="kn">as</span> <span class="nn">core</span>
+        <span class="n">d</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">core</span><span class="o">.</span><span class="n">__file__</span><span class="p">),</span> <span class="s">&#39;include&#39;</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">d</span>
+
+
+<span class="k">def</span> <span class="nf">_set_function_name</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+    <span class="n">func</span><span class="o">.</span><span class="n">__name__</span> <span class="o">=</span> <span class="n">name</span>
+    <span class="k">return</span> <span class="n">func</span>
+
+
+<span class="k">class</span> <span class="nc">_Deprecate</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Decorator class to deprecate old functions.</span>
+
+<span class="sd">    Refer to `deprecate` for details.</span>
+
+<span class="sd">    See Also</span>
+<span class="sd">    --------</span>
+<span class="sd">    deprecate</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">old_name</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">new_name</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">message</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">old_name</span> <span class="o">=</span> <span class="n">old_name</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">new_name</span> <span class="o">=</span> <span class="n">new_name</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">message</span> <span class="o">=</span> <span class="n">message</span>
+
+    <span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">func</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Decorator call.  Refer to ``decorate``.</span>
+
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">old_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">old_name</span>
+        <span class="n">new_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">new_name</span>
+        <span class="n">message</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">message</span>
+
+        <span class="kn">import</span> <span class="nn">warnings</span>
+        <span class="k">if</span> <span class="n">old_name</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+            <span class="k">try</span><span class="p">:</span>
+                <span class="n">old_name</span> <span class="o">=</span> <span class="n">func</span><span class="o">.</span><span class="n">__name__</span>
+            <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
+                <span class="n">old_name</span> <span class="o">=</span> <span class="n">func</span><span class="o">.</span><span class="n">__name__</span>
+        <span class="k">if</span> <span class="n">new_name</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+            <span class="n">depdoc</span> <span class="o">=</span> <span class="s">&quot;`</span><span class="si">%s</span><span class="s">` is deprecated!&quot;</span> <span class="o">%</span> <span class="n">old_name</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">depdoc</span> <span class="o">=</span> <span class="s">&quot;`</span><span class="si">%s</span><span class="s">` is deprecated, use `</span><span class="si">%s</span><span class="s">` instead!&quot;</span> <span class="o">%</span> \
+                     <span class="p">(</span><span class="n">old_name</span><span class="p">,</span> <span class="n">new_name</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">message</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
+            <span class="n">depdoc</span> <span class="o">+=</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span> <span class="o">+</span> <span class="n">message</span>
+
+        <span class="k">def</span> <span class="nf">newfunc</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span><span class="o">**</span><span class="n">kwds</span><span class="p">):</span>
+            <span class="sd">&quot;&quot;&quot;`arrayrange` is deprecated, use `arange` instead!&quot;&quot;&quot;</span>
+            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="n">depdoc</span><span class="p">,</span> <span class="ne">DeprecationWarning</span><span class="p">)</span>
+            <span class="k">return</span> <span class="n">func</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwds</span><span class="p">)</span>
+
+        <span class="n">newfunc</span> <span class="o">=</span> <span class="n">_set_function_name</span><span class="p">(</span><span class="n">newfunc</span><span class="p">,</span> <span class="n">old_name</span><span class="p">)</span>
+        <span class="n">doc</span> <span class="o">=</span> <span class="n">func</span><span class="o">.</span><span class="n">__doc__</span>
+        <span class="k">if</span> <span class="n">doc</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">=</span> <span class="n">depdoc</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">=</span> <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">depdoc</span><span class="p">,</span> <span class="n">doc</span><span class="p">])</span>
+        <span class="n">newfunc</span><span class="o">.</span><span class="n">__doc__</span> <span class="o">=</span> <span class="n">doc</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">d</span> <span class="o">=</span> <span class="n">func</span><span class="o">.</span><span class="n">__dict__</span>
+        <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
+            <span class="k">pass</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">newfunc</span><span class="o">.</span><span class="n">__dict__</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">newfunc</span>
+
+<span class="k">def</span> <span class="nf">deprecate</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Issues a DeprecationWarning, adds warning to `old_name`&#39;s</span>
+<span class="sd">    docstring, rebinds ``old_name.__name__`` and returns the new</span>
+<span class="sd">    function object.</span>
+
+<span class="sd">    This function may also be used as a decorator.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    func : function</span>
+<span class="sd">        The function to be deprecated.</span>
+<span class="sd">    old_name : str, optional</span>
+<span class="sd">        The name of the function to be deprecated. Default is None, in</span>
+<span class="sd">        which case the name of `func` is used.</span>
+<span class="sd">    new_name : str, optional</span>
+<span class="sd">        The new name for the function. Default is None, in which case the</span>
+<span class="sd">        deprecation message is that `old_name` is deprecated. If given, the</span>
+<span class="sd">        deprecation message is that `old_name` is deprecated and `new_name`</span>
+<span class="sd">        should be used instead.</span>
+<span class="sd">    message : str, optional</span>
+<span class="sd">        Additional explanation of the deprecation.  Displayed in the</span>
+<span class="sd">        docstring after the warning.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    old_func : function</span>
+<span class="sd">        The deprecated function.</span>
+
+<span class="sd">    Examples</span>
+<span class="sd">    --------</span>
+<span class="sd">    Note that ``olduint`` returns a value after printing Deprecation</span>
+<span class="sd">    Warning:</span>
+
+<span class="sd">    &gt;&gt;&gt; olduint = np.deprecate(np.uint)</span>
+<span class="sd">    &gt;&gt;&gt; olduint(6)</span>
+<span class="sd">    /usr/lib/python2.5/site-packages/numpy/lib/utils.py:114:</span>
+<span class="sd">    DeprecationWarning: uint32 is deprecated</span>
+<span class="sd">      warnings.warn(str1, DeprecationWarning)</span>
+<span class="sd">    6</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c"># Deprecate may be run as a function or as a decorator</span>
+    <span class="c"># If run as a function, we initialise the decorator class</span>
+    <span class="c"># and execute its __call__ method.</span>
+
+    <span class="k">if</span> <span class="n">args</span><span class="p">:</span>
+        <span class="n">fn</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">args</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
+
+        <span class="c"># backward compatibility -- can be removed</span>
+        <span class="c"># after next release</span>
+        <span class="k">if</span> <span class="s">&#39;newname&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+            <span class="n">kwargs</span><span class="p">[</span><span class="s">&#39;new_name&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;newname&#39;</span><span class="p">)</span>
+        <span class="k">if</span> <span class="s">&#39;oldname&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+            <span class="n">kwargs</span><span class="p">[</span><span class="s">&#39;old_name&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s">&#39;oldname&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">_Deprecate</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)(</span><span class="n">fn</span><span class="p">)</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">_Deprecate</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+<span class="n">deprecate_with_doc</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">msg</span><span class="p">:</span> <span class="n">_Deprecate</span><span class="p">(</span><span class="n">message</span><span class="o">=</span><span class="n">msg</span><span class="p">)</span>
+
+
+<span class="c">#--------------------------------------------</span>
+<span class="c"># Determine if two arrays can share memory</span>
+<span class="c">#--------------------------------------------</span>
+
+<span class="k">def</span> <span class="nf">byte_bounds</span><span class="p">(</span><span class="n">a</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns pointers to the end-points of an array.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    a : ndarray</span>
+<span class="sd">        Input array. It must conform to the Python-side of the array</span>
+<span class="sd">        interface.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    (low, high) : tuple of 2 integers</span>
+<span class="sd">        The first integer is the first byte of the array, the second</span>
+<span class="sd">        integer is just past the last byte of the array.  If `a` is not</span>
+<span class="sd">        contiguous it will not use every byte between the (`low`, `high`)</span>
+<span class="sd">        values.</span>
+
+<span class="sd">    Examples</span>
+<span class="sd">    --------</span>
+<span class="sd">    &gt;&gt;&gt; I = np.eye(2, dtype=&#39;f&#39;); I.dtype</span>
+<span class="sd">    dtype(&#39;float32&#39;)</span>
+<span class="sd">    &gt;&gt;&gt; low, high = np.byte_bounds(I)</span>
+<span class="sd">    &gt;&gt;&gt; high - low == I.size*I.itemsize</span>
+<span class="sd">    True</span>
+<span class="sd">    &gt;&gt;&gt; I = np.eye(2, dtype=&#39;G&#39;); I.dtype</span>
+<span class="sd">    dtype(&#39;complex192&#39;)</span>
+<span class="sd">    &gt;&gt;&gt; low, high = np.byte_bounds(I)</span>
+<span class="sd">    &gt;&gt;&gt; high - low == I.size*I.itemsize</span>
+<span class="sd">    True</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">ai</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">__array_interface__</span>
+    <span class="n">a_data</span> <span class="o">=</span> <span class="n">ai</span><span class="p">[</span><span class="s">&#39;data&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+    <span class="n">astrides</span> <span class="o">=</span> <span class="n">ai</span><span class="p">[</span><span class="s">&#39;strides&#39;</span><span class="p">]</span>
+    <span class="n">ashape</span> <span class="o">=</span> <span class="n">ai</span><span class="p">[</span><span class="s">&#39;shape&#39;</span><span class="p">]</span>
+    <span class="n">bytes_a</span> <span class="o">=</span> <span class="n">asarray</span><span class="p">(</span><span class="n">a</span><span class="p">)</span><span class="o">.</span><span class="n">dtype</span><span class="o">.</span><span class="n">itemsize</span>
+
+    <span class="n">a_low</span> <span class="o">=</span> <span class="n">a_high</span> <span class="o">=</span> <span class="n">a_data</span>
+    <span class="k">if</span> <span class="n">astrides</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+        <span class="c"># contiguous case</span>
+        <span class="n">a_high</span> <span class="o">+=</span> <span class="n">a</span><span class="o">.</span><span class="n">size</span> <span class="o">*</span> <span class="n">bytes_a</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">for</span> <span class="n">shape</span><span class="p">,</span> <span class="n">stride</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">ashape</span><span class="p">,</span> <span class="n">astrides</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">stride</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span>
+                <span class="n">a_low</span> <span class="o">+=</span> <span class="p">(</span><span class="n">shape</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="n">stride</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">a_high</span> <span class="o">+=</span> <span class="p">(</span><span class="n">shape</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="n">stride</span>
+        <span class="n">a_high</span> <span class="o">+=</span> <span class="n">bytes_a</span>
+    <span class="k">return</span> <span class="n">a_low</span><span class="p">,</span> <span class="n">a_high</span>
+
+
+<span class="c">#-----------------------------------------------------------------------------</span>
+<span class="c"># Function for output and information on the variables used.</span>
+<span class="c">#-----------------------------------------------------------------------------</span>
+
+
+<span class="k">def</span> <span class="nf">who</span><span class="p">(</span><span class="n">vardict</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Print the Numpy arrays in the given dictionary.</span>
+
+<span class="sd">    If there is no dictionary passed in or `vardict` is None then returns</span>
+<span class="sd">    Numpy arrays in the globals() dictionary (all Numpy arrays in the</span>
+<span class="sd">    namespace).</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    vardict : dict, optional</span>
+<span class="sd">        A dictionary possibly containing ndarrays.  Default is globals().</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    out : None</span>
+<span class="sd">        Returns &#39;None&#39;.</span>
+
+<span class="sd">    Notes</span>
+<span class="sd">    -----</span>
+<span class="sd">    Prints out the name, shape, bytes and type of all of the ndarrays</span>
+<span class="sd">    present in `vardict`.</span>
+
+<span class="sd">    Examples</span>
+<span class="sd">    --------</span>
+<span class="sd">    &gt;&gt;&gt; a = np.arange(10)</span>
+<span class="sd">    &gt;&gt;&gt; b = np.ones(20)</span>
+<span class="sd">    &gt;&gt;&gt; np.who()</span>
+<span class="sd">    Name            Shape            Bytes            Type</span>
+<span class="sd">    ===========================================================</span>
+<span class="sd">    a               10               40               int32</span>
+<span class="sd">    b               20               160              float64</span>
+<span class="sd">    Upper bound on total bytes  =       200</span>
+
+<span class="sd">    &gt;&gt;&gt; d = {&#39;x&#39;: np.arange(2.0), &#39;y&#39;: np.arange(3.0), &#39;txt&#39;: &#39;Some str&#39;,</span>
+<span class="sd">    ... &#39;idx&#39;:5}</span>
+<span class="sd">    &gt;&gt;&gt; np.who(d)</span>
+<span class="sd">    Name            Shape            Bytes            Type</span>
+<span class="sd">    ===========================================================</span>
+<span class="sd">    y               3                24               float64</span>
+<span class="sd">    x               2                16               float64</span>
+<span class="sd">    Upper bound on total bytes  =       40</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="n">vardict</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+        <span class="n">frame</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">_getframe</span><span class="p">()</span><span class="o">.</span><span class="n">f_back</span>
+        <span class="n">vardict</span> <span class="o">=</span> <span class="n">frame</span><span class="o">.</span><span class="n">f_globals</span>
+    <span class="n">sta</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">cache</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">vardict</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">vardict</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="n">ndarray</span><span class="p">):</span>
+            <span class="n">var</span> <span class="o">=</span> <span class="n">vardict</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
+            <span class="n">idv</span> <span class="o">=</span> <span class="nb">id</span><span class="p">(</span><span class="n">var</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">idv</span> <span class="ow">in</span> <span class="n">cache</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+                <span class="n">namestr</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s">&quot; (</span><span class="si">%s</span><span class="s">)&quot;</span> <span class="o">%</span> <span class="n">cache</span><span class="p">[</span><span class="n">idv</span><span class="p">]</span>
+                <span class="n">original</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">cache</span><span class="p">[</span><span class="n">idv</span><span class="p">]</span> <span class="o">=</span> <span class="n">name</span>
+                <span class="n">namestr</span> <span class="o">=</span> <span class="n">name</span>
+                <span class="n">original</span> <span class="o">=</span> <span class="mi">1</span>
+            <span class="n">shapestr</span> <span class="o">=</span> <span class="s">&quot; x &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">var</span><span class="o">.</span><span class="n">shape</span><span class="p">))</span>
+            <span class="n">bytestr</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">var</span><span class="o">.</span><span class="n">nbytes</span><span class="p">)</span>
+            <span class="n">sta</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">namestr</span><span class="p">,</span> <span class="n">shapestr</span><span class="p">,</span> <span class="n">bytestr</span><span class="p">,</span> <span class="n">var</span><span class="o">.</span><span class="n">dtype</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                        <span class="n">original</span><span class="p">])</span>
+
+    <span class="n">maxname</span> <span class="o">=</span> <span class="mi">0</span>
+    <span class="n">maxshape</span> <span class="o">=</span> <span class="mi">0</span>
+    <span class="n">maxbyte</span> <span class="o">=</span> <span class="mi">0</span>
+    <span class="n">totalbytes</span> <span class="o">=</span> <span class="mi">0</span>
+    <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">sta</span><span class="p">)):</span>
+        <span class="n">val</span> <span class="o">=</span> <span class="n">sta</span><span class="p">[</span><span class="n">k</span><span class="p">]</span>
+        <span class="k">if</span> <span class="n">maxname</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
+            <span class="n">maxname</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+        <span class="k">if</span> <span class="n">maxshape</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span>
+            <span class="n">maxshape</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+        <span class="k">if</span> <span class="n">maxbyte</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">2</span><span class="p">]):</span>
+            <span class="n">maxbyte</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+        <span class="k">if</span> <span class="n">val</span><span class="p">[</span><span class="mi">4</span><span class="p">]:</span>
+            <span class="n">totalbytes</span> <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sta</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="n">sp1</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="n">maxname</span><span class="p">)</span>
+        <span class="n">sp2</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="n">maxshape</span><span class="p">)</span>
+        <span class="n">sp3</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="n">maxbyte</span><span class="p">)</span>
+        <span class="n">prval</span> <span class="o">=</span> <span class="s">&quot;Name </span><span class="si">%s</span><span class="s"> Shape </span><span class="si">%s</span><span class="s"> Bytes </span><span class="si">%s</span><span class="s"> Type&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">sp1</span><span class="o">*</span><span class="s">&#39; &#39;</span><span class="p">,</span> <span class="n">sp2</span><span class="o">*</span><span class="s">&#39; &#39;</span><span class="p">,</span> <span class="n">sp3</span><span class="o">*</span><span class="s">&#39; &#39;</span><span class="p">)</span>
+        <span class="k">print</span><span class="p">(</span><span class="n">prval</span> <span class="o">+</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span> <span class="o">+</span> <span class="s">&quot;=&quot;</span><span class="o">*</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">prval</span><span class="p">)</span><span class="o">+</span><span class="mi">5</span><span class="p">)</span> <span class="o">+</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">sta</span><span class="p">)):</span>
+        <span class="n">val</span> <span class="o">=</span> <span class="n">sta</span><span class="p">[</span><span class="n">k</span><span class="p">]</span>
+        <span class="k">print</span><span class="p">(</span><span class="s">&quot;</span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">&#39; &#39;</span><span class="o">*</span><span class="p">(</span><span class="n">sp1</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span><span class="o">+</span><span class="mi">4</span><span class="p">),</span>
+                                        <span class="n">val</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">&#39; &#39;</span><span class="o">*</span><span class="p">(</span><span class="n">sp2</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mi">5</span><span class="p">),</span>
+                                        <span class="n">val</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s">&#39; &#39;</span><span class="o">*</span><span class="p">(</span><span class="n">sp3</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span><span class="o">+</span><span class="mi">5</span><span class="p">),</span>
+                                        <span class="n">val</span><span class="p">[</span><span class="mi">3</span><span class="p">]))</span>
+    <span class="k">print</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\n</span><span class="s">Upper bound on total bytes  =       </span><span class="si">%d</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">totalbytes</span><span class="p">)</span>
+    <span class="k">return</span>
+
+<span class="c">#-----------------------------------------------------------------------------</span>
+
+
+<span class="c"># NOTE:  pydoc defines a help function which works simliarly to this</span>
+<span class="c">#  except it uses a pager to take over the screen.</span>
+
+<span class="c"># combine name and arguments and split to multiple lines of width</span>
+<span class="c"># characters.  End lines on a comma and begin argument list indented with</span>
+<span class="c"># the rest of the arguments.</span>
+<span class="k">def</span> <span class="nf">_split_line</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">width</span><span class="p">):</span>
+    <span class="n">firstwidth</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+    <span class="n">k</span> <span class="o">=</span> <span class="n">firstwidth</span>
+    <span class="n">newstr</span> <span class="o">=</span> <span class="n">name</span>
+    <span class="n">sepstr</span> <span class="o">=</span> <span class="s">&quot;, &quot;</span>
+    <span class="n">arglist</span> <span class="o">=</span> <span class="n">arguments</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">sepstr</span><span class="p">)</span>
+    <span class="k">for</span> <span class="n">argument</span> <span class="ow">in</span> <span class="n">arglist</span><span class="p">:</span>
+        <span class="k">if</span> <span class="n">k</span> <span class="o">==</span> <span class="n">firstwidth</span><span class="p">:</span>
+            <span class="n">addstr</span> <span class="o">=</span> <span class="s">&quot;&quot;</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">addstr</span> <span class="o">=</span> <span class="n">sepstr</span>
+        <span class="n">k</span> <span class="o">=</span> <span class="n">k</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">argument</span><span class="p">)</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">addstr</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">k</span> <span class="o">&gt;</span> <span class="n">width</span><span class="p">:</span>
+            <span class="n">k</span> <span class="o">=</span> <span class="n">firstwidth</span> <span class="o">+</span> <span class="mi">1</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">argument</span><span class="p">)</span>
+            <span class="n">newstr</span> <span class="o">=</span> <span class="n">newstr</span> <span class="o">+</span> <span class="s">&quot;,</span><span class="se">\n</span><span class="s">&quot;</span> <span class="o">+</span> <span class="s">&quot; &quot;</span><span class="o">*</span><span class="p">(</span><span class="n">firstwidth</span><span class="o">+</span><span class="mi">2</span><span class="p">)</span> <span class="o">+</span> <span class="n">argument</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">newstr</span> <span class="o">=</span> <span class="n">newstr</span> <span class="o">+</span> <span class="n">addstr</span> <span class="o">+</span> <span class="n">argument</span>
+    <span class="k">return</span> <span class="n">newstr</span>
+
+<span class="n">_namedict</span> <span class="o">=</span> <span class="bp">None</span>
+<span class="n">_dictlist</span> <span class="o">=</span> <span class="bp">None</span>
+
+<span class="c"># Traverse all module directories underneath globals</span>
+<span class="c"># to see if something is defined</span>
+<span class="k">def</span> <span class="nf">_makenamedict</span><span class="p">(</span><span class="n">module</span><span class="o">=</span><span class="s">&#39;numpy&#39;</span><span class="p">):</span>
+    <span class="n">module</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">module</span><span class="p">,</span> <span class="nb">globals</span><span class="p">(),</span> <span class="nb">locals</span><span class="p">(),</span> <span class="p">[])</span>
+    <span class="n">thedict</span> <span class="o">=</span> <span class="p">{</span><span class="n">module</span><span class="o">.</span><span class="n">__name__</span><span class="p">:</span><span class="n">module</span><span class="o">.</span><span class="n">__dict__</span><span class="p">}</span>
+    <span class="n">dictlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">module</span><span class="o">.</span><span class="n">__name__</span><span class="p">]</span>
+    <span class="n">totraverse</span> <span class="o">=</span> <span class="p">[</span><span class="n">module</span><span class="o">.</span><span class="n">__dict__</span><span class="p">]</span>
+    <span class="k">while</span> <span class="bp">True</span><span class="p">:</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">totraverse</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="k">break</span>
+        <span class="n">thisdict</span> <span class="o">=</span> <span class="n">totraverse</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">thisdict</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">thisdict</span><span class="p">[</span><span class="n">x</span><span class="p">],</span> <span class="n">types</span><span class="o">.</span><span class="n">ModuleType</span><span class="p">):</span>
+                <span class="n">modname</span> <span class="o">=</span> <span class="n">thisdict</span><span class="p">[</span><span class="n">x</span><span class="p">]</span><span class="o">.</span><span class="n">__name__</span>
+                <span class="k">if</span> <span class="n">modname</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">dictlist</span><span class="p">:</span>
+                    <span class="n">moddict</span> <span class="o">=</span> <span class="n">thisdict</span><span class="p">[</span><span class="n">x</span><span class="p">]</span><span class="o">.</span><span class="n">__dict__</span>
+                    <span class="n">dictlist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">modname</span><span class="p">)</span>
+                    <span class="n">totraverse</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">moddict</span><span class="p">)</span>
+                    <span class="n">thedict</span><span class="p">[</span><span class="n">modname</span><span class="p">]</span> <span class="o">=</span> <span class="n">moddict</span>
+    <span class="k">return</span> <span class="n">thedict</span><span class="p">,</span> <span class="n">dictlist</span>
+
+
+<span class="k">def</span> <span class="nf">_info</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">output</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;Provide information about ndarray obj.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    obj: ndarray</span>
+<span class="sd">        Must be ndarray, not checked.</span>
+<span class="sd">    output:</span>
+<span class="sd">        Where printed output goes.</span>
+
+<span class="sd">    Notes</span>
+<span class="sd">    -----</span>
+<span class="sd">    Copied over from the numarray module prior to its removal.</span>
+<span class="sd">    Adapted somewhat as only numpy is an option now.</span>
+
+<span class="sd">    Called by info.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">extra</span> <span class="o">=</span> <span class="s">&quot;&quot;</span>
+    <span class="n">tic</span> <span class="o">=</span> <span class="s">&quot;&quot;</span>
+    <span class="n">bp</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span>
+    <span class="n">cls</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="s">&#39;__class__&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="p">(</span><span class="n">obj</span><span class="p">))</span>
+    <span class="n">nm</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">cls</span><span class="p">,</span> <span class="s">&#39;__name__&#39;</span><span class="p">,</span> <span class="n">cls</span><span class="p">)</span>
+    <span class="n">strides</span> <span class="o">=</span> <span class="n">obj</span><span class="o">.</span><span class="n">strides</span>
+    <span class="n">endian</span> <span class="o">=</span> <span class="n">obj</span><span class="o">.</span><span class="n">dtype</span><span class="o">.</span><span class="n">byteorder</span>
+
+    <span class="k">print</span><span class="p">(</span><span class="s">&quot;class: &quot;</span><span class="p">,</span> <span class="n">nm</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+    <span class="k">print</span><span class="p">(</span><span class="s">&quot;shape: &quot;</span><span class="p">,</span> <span class="n">obj</span><span class="o">.</span><span class="n">shape</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+    <span class="k">print</span><span class="p">(</span><span class="s">&quot;strides: &quot;</span><span class="p">,</span> <span class="n">strides</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+    <span class="k">print</span><span class="p">(</span><span class="s">&quot;itemsize: &quot;</span><span class="p">,</span> <span class="n">obj</span><span class="o">.</span><span class="n">itemsize</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+    <span class="k">print</span><span class="p">(</span><span class="s">&quot;aligned: &quot;</span><span class="p">,</span> <span class="n">bp</span><span class="p">(</span><span class="n">obj</span><span class="o">.</span><span class="n">flags</span><span class="o">.</span><span class="n">aligned</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+    <span class="k">print</span><span class="p">(</span><span class="s">&quot;contiguous: &quot;</span><span class="p">,</span> <span class="n">bp</span><span class="p">(</span><span class="n">obj</span><span class="o">.</span><span class="n">flags</span><span class="o">.</span><span class="n">contiguous</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+    <span class="k">print</span><span class="p">(</span><span class="s">&quot;fortran: &quot;</span><span class="p">,</span> <span class="n">obj</span><span class="o">.</span><span class="n">flags</span><span class="o">.</span><span class="n">fortran</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+    <span class="k">print</span><span class="p">(</span>
+        <span class="s">&quot;data pointer: </span><span class="si">%s%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">hex</span><span class="p">(</span><span class="n">obj</span><span class="o">.</span><span class="n">ctypes</span><span class="o">.</span><span class="n">_as_parameter_</span><span class="o">.</span><span class="n">value</span><span class="p">),</span> <span class="n">extra</span><span class="p">),</span>
+        <span class="nb">file</span><span class="o">=</span><span class="n">output</span>
+        <span class="p">)</span>
+    <span class="k">print</span><span class="p">(</span><span class="s">&quot;byteorder: &quot;</span><span class="p">,</span> <span class="n">end</span><span class="o">=</span><span class="s">&#39; &#39;</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+    <span class="k">if</span> <span class="n">endian</span> <span class="ow">in</span> <span class="p">[</span><span class="s">&#39;|&#39;</span><span class="p">,</span> <span class="s">&#39;=&#39;</span><span class="p">]:</span>
+        <span class="k">print</span><span class="p">(</span><span class="s">&quot;</span><span class="si">%s%s%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">tic</span><span class="p">,</span> <span class="n">sys</span><span class="o">.</span><span class="n">byteorder</span><span class="p">,</span> <span class="n">tic</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+        <span class="n">byteswap</span> <span class="o">=</span> <span class="bp">False</span>
+    <span class="k">elif</span> <span class="n">endian</span> <span class="o">==</span> <span class="s">&#39;&gt;&#39;</span><span class="p">:</span>
+        <span class="k">print</span><span class="p">(</span><span class="s">&quot;</span><span class="si">%s</span><span class="s">big</span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">tic</span><span class="p">,</span> <span class="n">tic</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+        <span class="n">byteswap</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">byteorder</span> <span class="o">!=</span> <span class="s">&quot;big&quot;</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">print</span><span class="p">(</span><span class="s">&quot;</span><span class="si">%s</span><span class="s">little</span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">tic</span><span class="p">,</span> <span class="n">tic</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+        <span class="n">byteswap</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">byteorder</span> <span class="o">!=</span> <span class="s">&quot;little&quot;</span>
+    <span class="k">print</span><span class="p">(</span><span class="s">&quot;byteswap: &quot;</span><span class="p">,</span> <span class="n">bp</span><span class="p">(</span><span class="n">byteswap</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+    <span class="k">print</span><span class="p">(</span><span class="s">&quot;type: </span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">obj</span><span class="o">.</span><span class="n">dtype</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+
+
+<span class="k">def</span> <span class="nf">info</span><span class="p">(</span><span class="nb">object</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">maxwidth</span><span class="o">=</span><span class="mi">76</span><span class="p">,</span> <span class="n">output</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="n">toplevel</span><span class="o">=</span><span class="s">&#39;numpy&#39;</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Get help information for a function, class, or module.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    object : object or str, optional</span>
+<span class="sd">        Input object or name to get information about. If `object` is a</span>
+<span class="sd">        numpy object, its docstring is given. If it is a string, available</span>
+<span class="sd">        modules are searched for matching objects.  If None, information</span>
+<span class="sd">        about `info` itself is returned.</span>
+<span class="sd">    maxwidth : int, optional</span>
+<span class="sd">        Printing width.</span>
+<span class="sd">    output : file like object, optional</span>
+<span class="sd">        File like object that the output is written to, default is</span>
+<span class="sd">        ``stdout``.  The object has to be opened in &#39;w&#39; or &#39;a&#39; mode.</span>
+<span class="sd">    toplevel : str, optional</span>
+<span class="sd">        Start search at this level.</span>
+
+<span class="sd">    See Also</span>
+<span class="sd">    --------</span>
+<span class="sd">    source, lookfor</span>
+
+<span class="sd">    Notes</span>
+<span class="sd">    -----</span>
+<span class="sd">    When used interactively with an object, ``np.info(obj)`` is equivalent</span>
+<span class="sd">    to ``help(obj)`` on the Python prompt or ``obj?`` on the IPython</span>
+<span class="sd">    prompt.</span>
+
+<span class="sd">    Examples</span>
+<span class="sd">    --------</span>
+<span class="sd">    &gt;&gt;&gt; np.info(np.polyval) # doctest: +SKIP</span>
+<span class="sd">       polyval(p, x)</span>
+<span class="sd">         Evaluate the polynomial p at x.</span>
+<span class="sd">         ...</span>
+
+<span class="sd">    When using a string for `object` it is possible to get multiple results.</span>
+
+<span class="sd">    &gt;&gt;&gt; np.info(&#39;fft&#39;) # doctest: +SKIP</span>
+<span class="sd">         *** Found in numpy ***</span>
+<span class="sd">    Core FFT routines</span>
+<span class="sd">    ...</span>
+<span class="sd">         *** Found in numpy.fft ***</span>
+<span class="sd">     fft(a, n=None, axis=-1)</span>
+<span class="sd">    ...</span>
+<span class="sd">         *** Repeat reference found in numpy.fft.fftpack ***</span>
+<span class="sd">         *** Total of 3 references found. ***</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">global</span> <span class="n">_namedict</span><span class="p">,</span> <span class="n">_dictlist</span>
+    <span class="c"># Local import to speed up numpy&#39;s import time.</span>
+    <span class="kn">import</span> <span class="nn">pydoc</span>
+    <span class="kn">import</span> <span class="nn">inspect</span>
+
+    <span class="k">if</span> <span class="p">(</span><span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">&#39;_ppimport_importer&#39;</span><span class="p">)</span> <span class="ow">or</span>
+           <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">&#39;_ppimport_module&#39;</span><span class="p">)):</span>
+        <span class="nb">object</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">_ppimport_module</span>
+    <span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">&#39;_ppimport_attr&#39;</span><span class="p">):</span>
+        <span class="nb">object</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">_ppimport_attr</span>
+
+    <span class="k">if</span> <span class="nb">object</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+        <span class="n">info</span><span class="p">(</span><span class="n">info</span><span class="p">)</span>
+    <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">ndarray</span><span class="p">):</span>
+        <span class="n">_info</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">output</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+    <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">_namedict</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+            <span class="n">_namedict</span><span class="p">,</span> <span class="n">_dictlist</span> <span class="o">=</span> <span class="n">_makenamedict</span><span class="p">(</span><span class="n">toplevel</span><span class="p">)</span>
+        <span class="n">numfound</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="n">objlist</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">for</span> <span class="n">namestr</span> <span class="ow">in</span> <span class="n">_dictlist</span><span class="p">:</span>
+            <span class="k">try</span><span class="p">:</span>
+                <span class="n">obj</span> <span class="o">=</span> <span class="n">_namedict</span><span class="p">[</span><span class="n">namestr</span><span class="p">][</span><span class="nb">object</span><span class="p">]</span>
+                <span class="k">if</span> <span class="nb">id</span><span class="p">(</span><span class="n">obj</span><span class="p">)</span> <span class="ow">in</span> <span class="n">objlist</span><span class="p">:</span>
+                    <span class="k">print</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\n</span><span class="s">     &quot;</span>
+                          <span class="s">&quot;*** Repeat reference found in </span><span class="si">%s</span><span class="s"> *** &quot;</span> <span class="o">%</span> <span class="n">namestr</span><span class="p">,</span>
+                          <span class="nb">file</span><span class="o">=</span><span class="n">output</span>
+                          <span class="p">)</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">objlist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">id</span><span class="p">(</span><span class="n">obj</span><span class="p">))</span>
+                    <span class="k">print</span><span class="p">(</span><span class="s">&quot;     *** Found in </span><span class="si">%s</span><span class="s"> ***&quot;</span> <span class="o">%</span> <span class="n">namestr</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+                    <span class="n">info</span><span class="p">(</span><span class="n">obj</span><span class="p">)</span>
+                    <span class="k">print</span><span class="p">(</span><span class="s">&quot;-&quot;</span><span class="o">*</span><span class="n">maxwidth</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+                <span class="n">numfound</span> <span class="o">+=</span> <span class="mi">1</span>
+            <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+                <span class="k">pass</span>
+        <span class="k">if</span> <span class="n">numfound</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="k">print</span><span class="p">(</span><span class="s">&quot;Help for </span><span class="si">%s</span><span class="s"> not found.&quot;</span> <span class="o">%</span> <span class="nb">object</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">print</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\n</span><span class="s">     &quot;</span>
+                  <span class="s">&quot;*** Total of </span><span class="si">%d</span><span class="s"> references found. ***&quot;</span> <span class="o">%</span> <span class="n">numfound</span><span class="p">,</span>
+                  <span class="nb">file</span><span class="o">=</span><span class="n">output</span>
+                  <span class="p">)</span>
+
+    <span class="k">elif</span> <span class="n">inspect</span><span class="o">.</span><span class="n">isfunction</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">__name__</span>
+        <span class="n">arguments</span> <span class="o">=</span> <span class="n">inspect</span><span class="o">.</span><span class="n">formatargspec</span><span class="p">(</span><span class="o">*</span><span class="n">inspect</span><span class="o">.</span><span class="n">getargspec</span><span class="p">(</span><span class="nb">object</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="o">+</span><span class="n">arguments</span><span class="p">)</span> <span class="o">&gt;</span> <span class="n">maxwidth</span><span class="p">:</span>
+            <span class="n">argstr</span> <span class="o">=</span> <span class="n">_split_line</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">maxwidth</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">argstr</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="n">arguments</span>
+
+        <span class="k">print</span><span class="p">(</span><span class="s">&quot; &quot;</span> <span class="o">+</span> <span class="n">argstr</span> <span class="o">+</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+        <span class="k">print</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="nb">object</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+
+    <span class="k">elif</span> <span class="n">inspect</span><span class="o">.</span><span class="n">isclass</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">__name__</span>
+        <span class="n">arguments</span> <span class="o">=</span> <span class="s">&quot;()&quot;</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">&#39;__init__&#39;</span><span class="p">):</span>
+                <span class="n">arguments</span> <span class="o">=</span> <span class="n">inspect</span><span class="o">.</span><span class="n">formatargspec</span><span class="p">(</span>
+                        <span class="o">*</span><span class="n">inspect</span><span class="o">.</span><span class="n">getargspec</span><span class="p">(</span><span class="nb">object</span><span class="o">.</span><span class="n">__init__</span><span class="o">.</span><span class="n">__func__</span><span class="p">)</span>
+                        <span class="p">)</span>
+                <span class="n">arglist</span> <span class="o">=</span> <span class="n">arguments</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;, &#39;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">arglist</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+                    <span class="n">arglist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="s">&quot;(&quot;</span><span class="o">+</span><span class="n">arglist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                    <span class="n">arguments</span> <span class="o">=</span> <span class="s">&quot;, &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">arglist</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span>
+        <span class="k">except</span><span class="p">:</span>
+            <span class="k">pass</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="o">+</span><span class="n">arguments</span><span class="p">)</span> <span class="o">&gt;</span> <span class="n">maxwidth</span><span class="p">:</span>
+            <span class="n">argstr</span> <span class="o">=</span> <span class="n">_split_line</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">maxwidth</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">argstr</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="n">arguments</span>
+
+        <span class="k">print</span><span class="p">(</span><span class="s">&quot; &quot;</span> <span class="o">+</span> <span class="n">argstr</span> <span class="o">+</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+        <span class="n">doc1</span> <span class="o">=</span> <span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">doc1</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">&#39;__init__&#39;</span><span class="p">):</span>
+                <span class="k">print</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="nb">object</span><span class="o">.</span><span class="n">__init__</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">print</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="nb">object</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+
+        <span class="n">methods</span> <span class="o">=</span> <span class="n">pydoc</span><span class="o">.</span><span class="n">allmethods</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">methods</span> <span class="o">!=</span> <span class="p">[]:</span>
+            <span class="k">print</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\n\n</span><span class="s">Methods:</span><span class="se">\n</span><span class="s">&quot;</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">meth</span> <span class="ow">in</span> <span class="n">methods</span><span class="p">:</span>
+                <span class="k">if</span> <span class="n">meth</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;_&#39;</span><span class="p">:</span>
+                    <span class="k">continue</span>
+                <span class="n">thisobj</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">meth</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">thisobj</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
+                    <span class="n">methstr</span><span class="p">,</span> <span class="n">other</span> <span class="o">=</span> <span class="n">pydoc</span><span class="o">.</span><span class="n">splitdoc</span><span class="p">(</span>
+                            <span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="n">thisobj</span><span class="p">)</span> <span class="ow">or</span> <span class="s">&quot;None&quot;</span>
+                            <span class="p">)</span>
+                <span class="k">print</span><span class="p">(</span><span class="s">&quot;  </span><span class="si">%s</span><span class="s">  --  </span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">meth</span><span class="p">,</span> <span class="n">methstr</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+
+    <span class="k">elif</span> <span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">version_info</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">&lt;</span> <span class="mi">3</span>
+            <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">types</span><span class="o">.</span><span class="n">InstanceType</span><span class="p">)):</span>
+        <span class="c"># check for __call__ method</span>
+        <span class="c"># types.InstanceType is the type of the instances of oldstyle classes</span>
+        <span class="k">print</span><span class="p">(</span><span class="s">&quot;Instance of class: &quot;</span><span class="p">,</span> <span class="nb">object</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+        <span class="k">print</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">&#39;__call__&#39;</span><span class="p">):</span>
+            <span class="n">arguments</span> <span class="o">=</span> <span class="n">inspect</span><span class="o">.</span><span class="n">formatargspec</span><span class="p">(</span>
+                    <span class="o">*</span><span class="n">inspect</span><span class="o">.</span><span class="n">getargspec</span><span class="p">(</span><span class="nb">object</span><span class="o">.</span><span class="n">__call__</span><span class="o">.</span><span class="n">__func__</span><span class="p">)</span>
+                    <span class="p">)</span>
+            <span class="n">arglist</span> <span class="o">=</span> <span class="n">arguments</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;, &#39;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">arglist</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+                <span class="n">arglist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="s">&quot;(&quot;</span><span class="o">+</span><span class="n">arglist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="n">arguments</span> <span class="o">=</span> <span class="s">&quot;, &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">arglist</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">arguments</span> <span class="o">=</span> <span class="s">&quot;()&quot;</span>
+
+            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">&#39;name&#39;</span><span class="p">):</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="s">&quot;</span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="nb">object</span><span class="o">.</span><span class="n">name</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="s">&quot;&lt;name&gt;&quot;</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="o">+</span><span class="n">arguments</span><span class="p">)</span> <span class="o">&gt;</span> <span class="n">maxwidth</span><span class="p">:</span>
+                <span class="n">argstr</span> <span class="o">=</span> <span class="n">_split_line</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">maxwidth</span><span class="p">)</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">argstr</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="n">arguments</span>
+
+            <span class="k">print</span><span class="p">(</span><span class="s">&quot; &quot;</span> <span class="o">+</span> <span class="n">argstr</span> <span class="o">+</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+            <span class="n">doc</span> <span class="o">=</span> <span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="nb">object</span><span class="o">.</span><span class="n">__call__</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">doc</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
+                <span class="k">print</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="nb">object</span><span class="o">.</span><span class="n">__call__</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+            <span class="k">print</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="nb">object</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">print</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="nb">object</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+
+    <span class="k">elif</span> <span class="n">inspect</span><span class="o">.</span><span class="n">ismethod</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">__name__</span>
+        <span class="n">arguments</span> <span class="o">=</span> <span class="n">inspect</span><span class="o">.</span><span class="n">formatargspec</span><span class="p">(</span>
+                <span class="o">*</span><span class="n">inspect</span><span class="o">.</span><span class="n">getargspec</span><span class="p">(</span><span class="nb">object</span><span class="o">.</span><span class="n">__func__</span><span class="p">)</span>
+                <span class="p">)</span>
+        <span class="n">arglist</span> <span class="o">=</span> <span class="n">arguments</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;, &#39;</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">arglist</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="n">arglist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="s">&quot;(&quot;</span><span class="o">+</span><span class="n">arglist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+            <span class="n">arguments</span> <span class="o">=</span> <span class="s">&quot;, &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">arglist</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">arguments</span> <span class="o">=</span> <span class="s">&quot;()&quot;</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="o">+</span><span class="n">arguments</span><span class="p">)</span> <span class="o">&gt;</span> <span class="n">maxwidth</span><span class="p">:</span>
+            <span class="n">argstr</span> <span class="o">=</span> <span class="n">_split_line</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">maxwidth</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">argstr</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="n">arguments</span>
+
+        <span class="k">print</span><span class="p">(</span><span class="s">&quot; &quot;</span> <span class="o">+</span> <span class="n">argstr</span> <span class="o">+</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+        <span class="k">print</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="nb">object</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+
+    <span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">&#39;__doc__&#39;</span><span class="p">):</span>
+        <span class="k">print</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="nb">object</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+
+
+<span class="k">def</span> <span class="nf">source</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">output</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Print or write to a file the source code for a Numpy object.</span>
+
+<span class="sd">    The source code is only returned for objects written in Python. Many</span>
+<span class="sd">    functions and classes are defined in C and will therefore not return</span>
+<span class="sd">    useful information.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    object : numpy object</span>
+<span class="sd">        Input object. This can be any object (function, class, module,</span>
+<span class="sd">        ...).</span>
+<span class="sd">    output : file object, optional</span>
+<span class="sd">        If `output` not supplied then source code is printed to screen</span>
+<span class="sd">        (sys.stdout).  File object must be created with either write &#39;w&#39; or</span>
+<span class="sd">        append &#39;a&#39; modes.</span>
+
+<span class="sd">    See Also</span>
+<span class="sd">    --------</span>
+<span class="sd">    lookfor, info</span>
+
+<span class="sd">    Examples</span>
+<span class="sd">    --------</span>
+<span class="sd">    &gt;&gt;&gt; np.source(np.interp)                        #doctest: +SKIP</span>
+<span class="sd">    In file: /usr/lib/python2.6/dist-packages/numpy/lib/function_base.py</span>
+<span class="sd">    def interp(x, xp, fp, left=None, right=None):</span>
+<span class="sd">        \&quot;\&quot;\&quot;.... (full docstring printed)\&quot;\&quot;\&quot;</span>
+<span class="sd">        if isinstance(x, (float, int, number)):</span>
+<span class="sd">            return compiled_interp([x], xp, fp, left, right).item()</span>
+<span class="sd">        else:</span>
+<span class="sd">            return compiled_interp(x, xp, fp, left, right)</span>
+
+<span class="sd">    The source code is only returned for objects written in Python.</span>
+
+<span class="sd">    &gt;&gt;&gt; np.source(np.array)                         #doctest: +SKIP</span>
+<span class="sd">    Not available for this object.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c"># Local import to speed up numpy&#39;s import time.</span>
+    <span class="kn">import</span> <span class="nn">inspect</span>
+    <span class="k">try</span><span class="p">:</span>
+        <span class="k">print</span><span class="p">(</span><span class="s">&quot;In file: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">inspect</span><span class="o">.</span><span class="n">getsourcefile</span><span class="p">(</span><span class="nb">object</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+        <span class="k">print</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">getsource</span><span class="p">(</span><span class="nb">object</span><span class="p">),</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+    <span class="k">except</span><span class="p">:</span>
+        <span class="k">print</span><span class="p">(</span><span class="s">&quot;Not available for this object.&quot;</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="n">output</span><span class="p">)</span>
+
+
+<span class="c"># Cache for lookfor: {id(module): {name: (docstring, kind, index), ...}...}</span>
+<span class="c"># where kind: &quot;func&quot;, &quot;class&quot;, &quot;module&quot;, &quot;object&quot;</span>
+<span class="c"># and index: index in breadth-first namespace traversal</span>
+<span class="n">_lookfor_caches</span> <span class="o">=</span> <span class="p">{}</span>
+
+<span class="c"># regexp whose match indicates that the string may contain a function</span>
+<span class="c"># signature</span>
+<span class="n">_function_signature_re</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="s">r&quot;[a-z0-9_]+\(.*[,=].*\)&quot;</span><span class="p">,</span> <span class="n">re</span><span class="o">.</span><span class="n">I</span><span class="p">)</span>
+
+<span class="k">def</span> <span class="nf">lookfor</span><span class="p">(</span><span class="n">what</span><span class="p">,</span> <span class="n">module</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">import_modules</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">regenerate</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
+            <span class="n">output</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Do a keyword search on docstrings.</span>
+
+<span class="sd">    A list of of objects that matched the search is displayed,</span>
+<span class="sd">    sorted by relevance. All given keywords need to be found in the</span>
+<span class="sd">    docstring for it to be returned as a result, but the order does</span>
+<span class="sd">    not matter.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    what : str</span>
+<span class="sd">        String containing words to look for.</span>
+<span class="sd">    module : str or list, optional</span>
+<span class="sd">        Name of module(s) whose docstrings to go through.</span>
+<span class="sd">    import_modules : bool, optional</span>
+<span class="sd">        Whether to import sub-modules in packages. Default is True.</span>
+<span class="sd">    regenerate : bool, optional</span>
+<span class="sd">        Whether to re-generate the docstring cache. Default is False.</span>
+<span class="sd">    output : file-like, optional</span>
+<span class="sd">        File-like object to write the output to. If omitted, use a pager.</span>
+
+<span class="sd">    See Also</span>
+<span class="sd">    --------</span>
+<span class="sd">    source, info</span>
+
+<span class="sd">    Notes</span>
+<span class="sd">    -----</span>
+<span class="sd">    Relevance is determined only roughly, by checking if the keywords occur</span>
+<span class="sd">    in the function name, at the start of a docstring, etc.</span>
+
+<span class="sd">    Examples</span>
+<span class="sd">    --------</span>
+<span class="sd">    &gt;&gt;&gt; np.lookfor(&#39;binary representation&#39;)</span>
+<span class="sd">    Search results for &#39;binary representation&#39;</span>
+<span class="sd">    ------------------------------------------</span>
+<span class="sd">    numpy.binary_repr</span>
+<span class="sd">        Return the binary representation of the input number as a string.</span>
+<span class="sd">    numpy.core.setup_common.long_double_representation</span>
+<span class="sd">        Given a binary dump as given by GNU od -b, look for long double</span>
+<span class="sd">    numpy.base_repr</span>
+<span class="sd">        Return a string representation of a number in the given base system.</span>
+<span class="sd">    ...</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="kn">import</span> <span class="nn">pydoc</span>
+
+    <span class="c"># Cache</span>
+    <span class="n">cache</span> <span class="o">=</span> <span class="n">_lookfor_generate_cache</span><span class="p">(</span><span class="n">module</span><span class="p">,</span> <span class="n">import_modules</span><span class="p">,</span> <span class="n">regenerate</span><span class="p">)</span>
+
+    <span class="c"># Search</span>
+    <span class="c"># XXX: maybe using a real stemming search engine would be better?</span>
+    <span class="n">found</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">whats</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">what</span><span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">whats</span><span class="p">:</span>
+        <span class="k">return</span>
+
+    <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="p">(</span><span class="n">docstring</span><span class="p">,</span> <span class="n">kind</span><span class="p">,</span> <span class="n">index</span><span class="p">)</span> <span class="ow">in</span> <span class="n">cache</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+        <span class="k">if</span> <span class="n">kind</span> <span class="ow">in</span> <span class="p">(</span><span class="s">&#39;module&#39;</span><span class="p">,</span> <span class="s">&#39;object&#39;</span><span class="p">):</span>
+            <span class="c"># don&#39;t show modules or objects</span>
+            <span class="k">continue</span>
+        <span class="n">ok</span> <span class="o">=</span> <span class="bp">True</span>
+        <span class="n">doc</span> <span class="o">=</span> <span class="n">docstring</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+        <span class="k">for</span> <span class="n">w</span> <span class="ow">in</span> <span class="n">whats</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">w</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">doc</span><span class="p">:</span>
+                <span class="n">ok</span> <span class="o">=</span> <span class="bp">False</span>
+                <span class="k">break</span>
+        <span class="k">if</span> <span class="n">ok</span><span class="p">:</span>
+            <span class="n">found</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+
+    <span class="c"># Relevance sort</span>
+    <span class="c"># XXX: this is full Harrison-Stetson heuristics now,</span>
+    <span class="c"># XXX: it probably could be improved</span>
+
+    <span class="n">kind_relevance</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;func&#39;</span><span class="p">:</span> <span class="mi">1000</span><span class="p">,</span> <span class="s">&#39;class&#39;</span><span class="p">:</span> <span class="mi">1000</span><span class="p">,</span>
+                      <span class="s">&#39;module&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mi">1000</span><span class="p">,</span> <span class="s">&#39;object&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mi">1000</span><span class="p">}</span>
+
+    <span class="k">def</span> <span class="nf">relevance</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">docstr</span><span class="p">,</span> <span class="n">kind</span><span class="p">,</span> <span class="n">index</span><span class="p">):</span>
+        <span class="n">r</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="c"># do the keywords occur within the start of the docstring?</span>
+        <span class="n">first_doc</span> <span class="o">=</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">docstr</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="p">)[:</span><span class="mi">3</span><span class="p">])</span>
+        <span class="n">r</span> <span class="o">+=</span> <span class="nb">sum</span><span class="p">([</span><span class="mi">200</span> <span class="k">for</span> <span class="n">w</span> <span class="ow">in</span> <span class="n">whats</span> <span class="k">if</span> <span class="n">w</span> <span class="ow">in</span> <span class="n">first_doc</span><span class="p">])</span>
+        <span class="c"># do the keywords occur in the function name?</span>
+        <span class="n">r</span> <span class="o">+=</span> <span class="nb">sum</span><span class="p">([</span><span class="mi">30</span> <span class="k">for</span> <span class="n">w</span> <span class="ow">in</span> <span class="n">whats</span> <span class="k">if</span> <span class="n">w</span> <span class="ow">in</span> <span class="n">name</span><span class="p">])</span>
+        <span class="c"># is the full name long?</span>
+        <span class="n">r</span> <span class="o">+=</span> <span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="p">)</span> <span class="o">*</span> <span class="mi">5</span>
+        <span class="c"># is the object of bad type?</span>
+        <span class="n">r</span> <span class="o">+=</span> <span class="n">kind_relevance</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">kind</span><span class="p">,</span> <span class="o">-</span><span class="mi">1000</span><span class="p">)</span>
+        <span class="c"># is the object deep in namespace hierarchy?</span>
+        <span class="n">r</span> <span class="o">+=</span> <span class="o">-</span><span class="n">name</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">&#39;.&#39;</span><span class="p">)</span> <span class="o">*</span> <span class="mi">10</span>
+        <span class="n">r</span> <span class="o">+=</span> <span class="nb">max</span><span class="p">(</span><span class="o">-</span><span class="n">index</span> <span class="o">/</span> <span class="mi">100</span><span class="p">,</span> <span class="o">-</span><span class="mi">100</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">r</span>
+
+    <span class="k">def</span> <span class="nf">relevance_value</span><span class="p">(</span><span class="n">a</span><span class="p">):</span>
+        <span class="k">return</span> <span class="n">relevance</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="o">*</span><span class="n">cache</span><span class="p">[</span><span class="n">a</span><span class="p">])</span>
+    <span class="n">found</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="n">relevance_value</span><span class="p">)</span>
+
+    <span class="c"># Pretty-print</span>
+    <span class="n">s</span> <span class="o">=</span> <span class="s">&quot;Search results for &#39;</span><span class="si">%s</span><span class="s">&#39;&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="s">&#39; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">whats</span><span class="p">))</span>
+    <span class="n">help_text</span> <span class="o">=</span> <span class="p">[</span><span class="n">s</span><span class="p">,</span> <span class="s">&quot;-&quot;</span><span class="o">*</span><span class="nb">len</span><span class="p">(</span><span class="n">s</span><span class="p">)]</span>
+    <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">found</span><span class="p">[::</span><span class="o">-</span><span class="mi">1</span><span class="p">]:</span>
+        <span class="n">doc</span><span class="p">,</span> <span class="n">kind</span><span class="p">,</span> <span class="n">ix</span> <span class="o">=</span> <span class="n">cache</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
+
+        <span class="n">doclines</span> <span class="o">=</span> <span class="p">[</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">doc</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()]</span>
+
+        <span class="c"># find a suitable short description</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">first_doc</span> <span class="o">=</span> <span class="n">doclines</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+            <span class="k">if</span> <span class="n">_function_signature_re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">first_doc</span><span class="p">):</span>
+                <span class="n">first_doc</span> <span class="o">=</span> <span class="n">doclines</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+        <span class="k">except</span> <span class="ne">IndexError</span><span class="p">:</span>
+            <span class="n">first_doc</span> <span class="o">=</span> <span class="s">&quot;&quot;</span>
+        <span class="n">help_text</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">&quot;</span><span class="si">%s</span><span class="se">\n</span><span class="s">    </span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">first_doc</span><span class="p">))</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">found</span><span class="p">:</span>
+        <span class="n">help_text</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">&quot;Nothing found.&quot;</span><span class="p">)</span>
+
+    <span class="c"># Output</span>
+    <span class="k">if</span> <span class="n">output</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
+        <span class="n">output</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">help_text</span><span class="p">))</span>
+    <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">help_text</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">10</span><span class="p">:</span>
+        <span class="n">pager</span> <span class="o">=</span> <span class="n">pydoc</span><span class="o">.</span><span class="n">getpager</span><span class="p">()</span>
+        <span class="n">pager</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">help_text</span><span class="p">))</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">print</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">help_text</span><span class="p">))</span>
+
+<span class="k">def</span> <span class="nf">_lookfor_generate_cache</span><span class="p">(</span><span class="n">module</span><span class="p">,</span> <span class="n">import_modules</span><span class="p">,</span> <span class="n">regenerate</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Generate docstring cache for given module.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    module : str, None, module</span>
+<span class="sd">        Module for which to generate docstring cache</span>
+<span class="sd">    import_modules : bool</span>
+<span class="sd">        Whether to import sub-modules in packages.</span>
+<span class="sd">    regenerate : bool</span>
+<span class="sd">        Re-generate the docstring cache</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    cache : dict {obj_full_name: (docstring, kind, index), ...}</span>
+<span class="sd">        Docstring cache for the module, either cached one (regenerate=False)</span>
+<span class="sd">        or newly generated.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">global</span> <span class="n">_lookfor_caches</span>
+    <span class="c"># Local import to speed up numpy&#39;s import time.</span>
+    <span class="kn">import</span> <span class="nn">inspect</span>
+
+    <span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">version_info</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">&gt;=</span> <span class="mi">3</span><span class="p">:</span>
+        <span class="c"># In Python3 stderr, stdout are text files.</span>
+        <span class="kn">from</span> <span class="nn">io</span> <span class="kn">import</span> <span class="n">StringIO</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="kn">from</span> <span class="nn">StringIO</span> <span class="kn">import</span> <span class="n">StringIO</span>
+
+    <span class="k">if</span> <span class="n">module</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
+        <span class="n">module</span> <span class="o">=</span> <span class="s">&quot;numpy&quot;</span>
+
+    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">module</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="nb">__import__</span><span class="p">(</span><span class="n">module</span><span class="p">)</span>
+        <span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
+            <span class="k">return</span> <span class="p">{}</span>
+        <span class="n">module</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="n">module</span><span class="p">]</span>
+    <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">module</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">module</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+        <span class="n">cache</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">for</span> <span class="n">mod</span> <span class="ow">in</span> <span class="n">module</span><span class="p">:</span>
+            <span class="n">cache</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">_lookfor_generate_cache</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="n">import_modules</span><span class="p">,</span>
+                                                 <span class="n">regenerate</span><span class="p">))</span>
+        <span class="k">return</span> <span class="n">cache</span>
+
+    <span class="k">if</span> <span class="nb">id</span><span class="p">(</span><span class="n">module</span><span class="p">)</span> <span class="ow">in</span> <span class="n">_lookfor_caches</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">regenerate</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">_lookfor_caches</span><span class="p">[</span><span class="nb">id</span><span class="p">(</span><span class="n">module</span><span class="p">)]</span>
+
+    <span class="c"># walk items and collect docstrings</span>
+    <span class="n">cache</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">_lookfor_caches</span><span class="p">[</span><span class="nb">id</span><span class="p">(</span><span class="n">module</span><span class="p">)]</span> <span class="o">=</span> <span class="n">cache</span>
+    <span class="n">seen</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">index</span> <span class="o">=</span> <span class="mi">0</span>
+    <span class="n">stack</span> <span class="o">=</span> <span class="p">[(</span><span class="n">module</span><span class="o">.</span><span class="n">__name__</span><span class="p">,</span> <span class="n">module</span><span class="p">)]</span>
+    <span class="k">while</span> <span class="n">stack</span><span class="p">:</span>
+        <span class="n">name</span><span class="p">,</span> <span class="n">item</span> <span class="o">=</span> <span class="n">stack</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">id</span><span class="p">(</span><span class="n">item</span><span class="p">)</span> <span class="ow">in</span> <span class="n">seen</span><span class="p">:</span>
+            <span class="k">continue</span>
+        <span class="n">seen</span><span class="p">[</span><span class="nb">id</span><span class="p">(</span><span class="n">item</span><span class="p">)]</span> <span class="o">=</span> <span class="bp">True</span>
+
+        <span class="n">index</span> <span class="o">+=</span> <span class="mi">1</span>
+        <span class="n">kind</span> <span class="o">=</span> <span class="s">&quot;object&quot;</span>
+
+        <span class="k">if</span> <span class="n">inspect</span><span class="o">.</span><span class="n">ismodule</span><span class="p">(</span><span class="n">item</span><span class="p">):</span>
+            <span class="n">kind</span> <span class="o">=</span> <span class="s">&quot;module&quot;</span>
+            <span class="k">try</span><span class="p">:</span>
+                <span class="n">_all</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">__all__</span>
+            <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
+                <span class="n">_all</span> <span class="o">=</span> <span class="bp">None</span>
+
+            <span class="c"># import sub-packages</span>
+            <span class="k">if</span> <span class="n">import_modules</span> <span class="ow">and</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="s">&#39;__path__&#39;</span><span class="p">):</span>
+                <span class="k">for</span> <span class="n">pth</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">__path__</span><span class="p">:</span>
+                    <span class="k">for</span> <span class="n">mod_path</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="n">pth</span><span class="p">):</span>
+                        <span class="n">this_py</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">pth</span><span class="p">,</span> <span class="n">mod_path</span><span class="p">)</span>
+                        <span class="n">init_py</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">pth</span><span class="p">,</span> <span class="n">mod_path</span><span class="p">,</span> <span class="s">&#39;__init__.py&#39;</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">this_py</span><span class="p">)</span> <span class="ow">and</span>
+                                <span class="n">mod_path</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s">&#39;.py&#39;</span><span class="p">)):</span>
+                            <span class="n">to_import</span> <span class="o">=</span> <span class="n">mod_path</span><span class="p">[:</span><span class="o">-</span><span class="mi">3</span><span class="p">]</span>
+                        <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">init_py</span><span class="p">):</span>
+                            <span class="n">to_import</span> <span class="o">=</span> <span class="n">mod_path</span>
+                        <span class="k">else</span><span class="p">:</span>
+                            <span class="k">continue</span>
+                        <span class="k">if</span> <span class="n">to_import</span> <span class="o">==</span> <span class="s">&#39;__init__&#39;</span><span class="p">:</span>
+                            <span class="k">continue</span>
+
+                        <span class="k">try</span><span class="p">:</span>
+                            <span class="c"># Catch SystemExit, too</span>
+                            <span class="n">base_exc</span> <span class="o">=</span> <span class="ne">BaseException</span>
+                        <span class="k">except</span> <span class="ne">NameError</span><span class="p">:</span>
+                            <span class="c"># Python 2.4 doesn&#39;t have BaseException</span>
+                            <span class="n">base_exc</span> <span class="o">=</span> <span class="ne">Exception</span>
+
+                        <span class="k">try</span><span class="p">:</span>
+                            <span class="n">old_stdout</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span>
+                            <span class="n">old_stderr</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span>
+                            <span class="k">try</span><span class="p">:</span>
+                                <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="n">StringIO</span><span class="p">()</span>
+                                <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="n">StringIO</span><span class="p">()</span>
+                                <span class="nb">__import__</span><span class="p">(</span><span class="s">&quot;</span><span class="si">%s</span><span class="s">.</span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">to_import</span><span class="p">))</span>
+                            <span class="k">finally</span><span class="p">:</span>
+                                <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="n">old_stdout</span>
+                                <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="n">old_stderr</span>
+                        <span class="k">except</span> <span class="n">base_exc</span><span class="p">:</span>
+                            <span class="k">continue</span>
+
+            <span class="k">for</span> <span class="n">n</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">_getmembers</span><span class="p">(</span><span class="n">item</span><span class="p">):</span>
+                <span class="k">try</span><span class="p">:</span>
+                    <span class="n">item_name</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="s">&#39;__name__&#39;</span><span class="p">,</span> <span class="s">&quot;</span><span class="si">%s</span><span class="s">.</span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">n</span><span class="p">))</span>
+                    <span class="n">mod_name</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="s">&#39;__module__&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
+                <span class="k">except</span> <span class="ne">NameError</span><span class="p">:</span>
+                    <span class="c"># ref. SWIG&#39;s global cvars</span>
+                    <span class="c">#    NameError: Unknown C global variable</span>
+                    <span class="n">item_name</span> <span class="o">=</span> <span class="s">&quot;</span><span class="si">%s</span><span class="s">.</span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">n</span><span class="p">)</span>
+                    <span class="n">mod_name</span> <span class="o">=</span> <span class="bp">None</span>
+                <span class="k">if</span> <span class="s">&#39;.&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">item_name</span> <span class="ow">and</span> <span class="n">mod_name</span><span class="p">:</span>
+                    <span class="n">item_name</span> <span class="o">=</span> <span class="s">&quot;</span><span class="si">%s</span><span class="s">.</span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">mod_name</span><span class="p">,</span> <span class="n">item_name</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">item_name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">name</span> <span class="o">+</span> <span class="s">&#39;.&#39;</span><span class="p">):</span>
+                    <span class="c"># don&#39;t crawl &quot;foreign&quot; objects</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">ufunc</span><span class="p">):</span>
+                        <span class="c"># ... unless they are ufuncs</span>
+                        <span class="k">pass</span>
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="k">continue</span>
+                <span class="k">elif</span> <span class="ow">not</span> <span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">ismodule</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="ow">or</span> <span class="n">_all</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">_all</span><span class="p">):</span>
+                    <span class="k">continue</span>
+                <span class="n">stack</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="s">&quot;</span><span class="si">%s</span><span class="s">.</span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">n</span><span class="p">),</span> <span class="n">v</span><span class="p">))</span>
+        <span class="k">elif</span> <span class="n">inspect</span><span class="o">.</span><span class="n">isclass</span><span class="p">(</span><span class="n">item</span><span class="p">):</span>
+            <span class="n">kind</span> <span class="o">=</span> <span class="s">&quot;class&quot;</span>
+            <span class="k">for</span> <span class="n">n</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">_getmembers</span><span class="p">(</span><span class="n">item</span><span class="p">):</span>
+                <span class="n">stack</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="s">&quot;</span><span class="si">%s</span><span class="s">.</span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">n</span><span class="p">),</span> <span class="n">v</span><span class="p">))</span>
+        <span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="s">&quot;__call__&quot;</span><span class="p">):</span>
+            <span class="n">kind</span> <span class="o">=</span> <span class="s">&quot;func&quot;</span>
+
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">=</span> <span class="n">inspect</span><span class="o">.</span><span class="n">getdoc</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
+        <span class="k">except</span> <span class="ne">NameError</span><span class="p">:</span>
+            <span class="c"># ref SWIG&#39;s NameError: Unknown C global variable</span>
+            <span class="n">doc</span> <span class="o">=</span> <span class="bp">None</span>
+        <span class="k">if</span> <span class="n">doc</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
+            <span class="n">cache</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">doc</span><span class="p">,</span> <span class="n">kind</span><span class="p">,</span> <span class="n">index</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">cache</span>
+
+<span class="k">def</span> <span class="nf">_getmembers</span><span class="p">(</span><span class="n">item</span><span class="p">):</span>
+    <span class="kn">import</span> <span class="nn">inspect</span>
+    <span class="k">try</span><span class="p">:</span>
+        <span class="n">members</span> <span class="o">=</span> <span class="n">inspect</span><span class="o">.</span><span class="n">getmembers</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
+    <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
+        <span class="n">members</span> <span class="o">=</span> <span class="p">[(</span><span class="n">x</span><span class="p">,</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">x</span><span class="p">))</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">dir</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
+                   <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">x</span><span class="p">)]</span>
+    <span class="k">return</span> <span class="n">members</span>
+
+<span class="c">#-----------------------------------------------------------------------------</span>
+
+<span class="c"># The following SafeEval class and company are adapted from Michael Spencer&#39;s</span>
+<span class="c"># ASPN Python Cookbook recipe:</span>
+<span class="c">#   http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/364469</span>
+<span class="c"># Accordingly it is mostly Copyright 2006 by Michael Spencer.</span>
+<span class="c"># The recipe, like most of the other ASPN Python Cookbook recipes was made</span>
+<span class="c"># available under the Python license.</span>
+<span class="c">#   http://www.python.org/license</span>
+
+<span class="c"># It has been modified to:</span>
+<span class="c">#   * handle unary -/+</span>
+<span class="c">#   * support True/False/None</span>
+<span class="c">#   * raise SyntaxError instead of a custom exception.</span>
+
+<span class="k">class</span> <span class="nc">SafeEval</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Object to evaluate constant string expressions.</span>
+
+<span class="sd">    This includes strings with lists, dicts and tuples using the abstract</span>
+<span class="sd">    syntax tree created by ``compiler.parse``.</span>
+
+<span class="sd">    For an example of usage, see `safe_eval`.</span>
+
+<span class="sd">    See Also</span>
+<span class="sd">    --------</span>
+<span class="sd">    safe_eval</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">version_info</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">&lt;</span> <span class="mi">3</span><span class="p">:</span>
+        <span class="k">def</span> <span class="nf">visit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+            <span class="n">cls</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">__class__</span>
+            <span class="n">meth</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">&#39;visit&#39;</span><span class="o">+</span><span class="n">cls</span><span class="o">.</span><span class="n">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">default</span><span class="p">)</span>
+            <span class="k">return</span> <span class="n">meth</span><span class="p">(</span><span class="n">node</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">default</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+            <span class="k">raise</span> <span class="ne">SyntaxError</span><span class="p">(</span><span class="s">&quot;Unsupported source construct: </span><span class="si">%s</span><span class="s">&quot;</span>
+                              <span class="o">%</span> <span class="n">node</span><span class="o">.</span><span class="n">__class__</span><span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">visitExpression</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+            <span class="k">for</span> <span class="n">child</span> <span class="ow">in</span> <span class="n">node</span><span class="o">.</span><span class="n">getChildNodes</span><span class="p">():</span>
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">child</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">visitConst</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+            <span class="k">return</span> <span class="n">node</span><span class="o">.</span><span class="n">value</span>
+
+        <span class="k">def</span> <span class="nf">visitDict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span><span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+            <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+                    <span class="p">[(</span><span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">k</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">v</span><span class="p">))</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">node</span><span class="o">.</span><span class="n">items</span><span class="p">]</span>
+                    <span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">visitTuple</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+            <span class="k">return</span> <span class="nb">tuple</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">node</span><span class="o">.</span><span class="n">nodes</span><span class="p">])</span>
+
+        <span class="k">def</span> <span class="nf">visitList</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+            <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">node</span><span class="o">.</span><span class="n">nodes</span><span class="p">]</span>
+
+        <span class="k">def</span> <span class="nf">visitUnaryAdd</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+            <span class="k">return</span> <span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">node</span><span class="o">.</span><span class="n">getChildNodes</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
+
+        <span class="k">def</span> <span class="nf">visitUnarySub</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+            <span class="k">return</span> <span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">node</span><span class="o">.</span><span class="n">getChildNodes</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
+
+        <span class="k">def</span> <span class="nf">visitName</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">node</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">&#39;False&#39;</span><span class="p">:</span>
+                <span class="k">return</span> <span class="bp">False</span>
+            <span class="k">elif</span> <span class="n">node</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">&#39;True&#39;</span><span class="p">:</span>
+                <span class="k">return</span> <span class="bp">True</span>
+            <span class="k">elif</span> <span class="n">node</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">&#39;None&#39;</span><span class="p">:</span>
+                <span class="k">return</span> <span class="bp">None</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="k">raise</span> <span class="ne">SyntaxError</span><span class="p">(</span><span class="s">&quot;Unknown name: </span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">node</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+    <span class="k">else</span><span class="p">:</span>
+
+        <span class="k">def</span> <span class="nf">visit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">):</span>
+            <span class="n">cls</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">__class__</span>
+            <span class="n">meth</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">&#39;visit&#39;</span> <span class="o">+</span> <span class="n">cls</span><span class="o">.</span><span class="n">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">default</span><span class="p">)</span>
+            <span class="k">return</span> <span class="n">meth</span><span class="p">(</span><span class="n">node</span><span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">default</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">):</span>
+            <span class="k">raise</span> <span class="ne">SyntaxError</span><span class="p">(</span><span class="s">&quot;Unsupported source construct: </span><span class="si">%s</span><span class="s">&quot;</span>
+                              <span class="o">%</span> <span class="n">node</span><span class="o">.</span><span class="n">__class__</span><span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">visitExpression</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">):</span>
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">node</span><span class="o">.</span><span class="n">body</span><span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">visitNum</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">):</span>
+            <span class="k">return</span> <span class="n">node</span><span class="o">.</span><span class="n">n</span>
+
+        <span class="k">def</span> <span class="nf">visitStr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">):</span>
+            <span class="k">return</span> <span class="n">node</span><span class="o">.</span><span class="n">s</span>
+
+        <span class="k">def</span> <span class="nf">visitBytes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">):</span>
+            <span class="k">return</span> <span class="n">node</span><span class="o">.</span><span class="n">s</span>
+
+        <span class="k">def</span> <span class="nf">visitDict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span><span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+            <span class="k">return</span> <span class="nb">dict</span><span class="p">([(</span><span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">k</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">v</span><span class="p">))</span>
+                         <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">node</span><span class="o">.</span><span class="n">keys</span><span class="p">,</span> <span class="n">node</span><span class="o">.</span><span class="n">values</span><span class="p">)])</span>
+
+        <span class="k">def</span> <span class="nf">visitTuple</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">):</span>
+            <span class="k">return</span> <span class="nb">tuple</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">node</span><span class="o">.</span><span class="n">elts</span><span class="p">])</span>
+
+        <span class="k">def</span> <span class="nf">visitList</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">):</span>
+            <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">node</span><span class="o">.</span><span class="n">elts</span><span class="p">]</span>
+
+        <span class="k">def</span> <span class="nf">visitUnaryOp</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">):</span>
+            <span class="kn">import</span> <span class="nn">ast</span>
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">node</span><span class="o">.</span><span class="n">op</span><span class="p">,</span> <span class="n">ast</span><span class="o">.</span><span class="n">UAdd</span><span class="p">):</span>
+                <span class="k">return</span> <span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">node</span><span class="o">.</span><span class="n">operand</span><span class="p">)</span>
+            <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">node</span><span class="o">.</span><span class="n">op</span><span class="p">,</span> <span class="n">ast</span><span class="o">.</span><span class="n">USub</span><span class="p">):</span>
+                <span class="k">return</span> <span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">node</span><span class="o">.</span><span class="n">operand</span><span class="p">)</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="k">raise</span> <span class="ne">SyntaxError</span><span class="p">(</span><span class="s">&quot;Unknown unary op: </span><span class="si">%r</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">node</span><span class="o">.</span><span class="n">op</span><span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">visitName</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">node</span><span class="o">.</span><span class="n">id</span> <span class="o">==</span> <span class="s">&#39;False&#39;</span><span class="p">:</span>
+                <span class="k">return</span> <span class="bp">False</span>
+            <span class="k">elif</span> <span class="n">node</span><span class="o">.</span><span class="n">id</span> <span class="o">==</span> <span class="s">&#39;True&#39;</span><span class="p">:</span>
+                <span class="k">return</span> <span class="bp">True</span>
+            <span class="k">elif</span> <span class="n">node</span><span class="o">.</span><span class="n">id</span> <span class="o">==</span> <span class="s">&#39;None&#39;</span><span class="p">:</span>
+                <span class="k">return</span> <span class="bp">None</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="k">raise</span> <span class="ne">SyntaxError</span><span class="p">(</span><span class="s">&quot;Unknown name: </span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">node</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">visitNameConstant</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">node</span><span class="p">):</span>
+            <span class="k">return</span> <span class="n">node</span><span class="o">.</span><span class="n">value</span>
+
+<span class="k">def</span> <span class="nf">safe_eval</span><span class="p">(</span><span class="n">source</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Protected string evaluation.</span>
+
+<span class="sd">    Evaluate a string containing a Python literal expression without</span>
+<span class="sd">    allowing the execution of arbitrary non-literal code.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    source : str</span>
+<span class="sd">        The string to evaluate.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    obj : object</span>
+<span class="sd">       The result of evaluating `source`.</span>
+
+<span class="sd">    Raises</span>
+<span class="sd">    ------</span>
+<span class="sd">    SyntaxError</span>
+<span class="sd">        If the code has invalid Python syntax, or if it contains</span>
+<span class="sd">        non-literal code.</span>
+
+<span class="sd">    Examples</span>
+<span class="sd">    --------</span>
+<span class="sd">    &gt;&gt;&gt; np.safe_eval(&#39;1&#39;)</span>
+<span class="sd">    1</span>
+<span class="sd">    &gt;&gt;&gt; np.safe_eval(&#39;[1, 2, 3]&#39;)</span>
+<span class="sd">    [1, 2, 3]</span>
+<span class="sd">    &gt;&gt;&gt; np.safe_eval(&#39;{&quot;foo&quot;: (&quot;bar&quot;, 10.0)}&#39;)</span>
+<span class="sd">    {&#39;foo&#39;: (&#39;bar&#39;, 10.0)}</span>
+
+<span class="sd">    &gt;&gt;&gt; np.safe_eval(&#39;import os&#39;)</span>
+<span class="sd">    Traceback (most recent call last):</span>
+<span class="sd">      ...</span>
+<span class="sd">    SyntaxError: invalid syntax</span>
+
+<span class="sd">    &gt;&gt;&gt; np.safe_eval(&#39;open(&quot;/home/user/.ssh/id_dsa&quot;).read()&#39;)</span>
+<span class="sd">    Traceback (most recent call last):</span>
+<span class="sd">      ...</span>
+<span class="sd">    SyntaxError: Unsupported source construct: compiler.ast.CallFunc</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c"># Local imports to speed up numpy&#39;s import time.</span>
+    <span class="kn">import</span> <span class="nn">warnings</span>
+
+    <span class="k">with</span> <span class="n">warnings</span><span class="o">.</span><span class="n">catch_warnings</span><span class="p">():</span>
+        <span class="c"># compiler package is deprecated for 3.x, which is already solved</span>
+        <span class="c"># here</span>
+        <span class="n">warnings</span><span class="o">.</span><span class="n">simplefilter</span><span class="p">(</span><span class="s">&#39;ignore&#39;</span><span class="p">,</span> <span class="ne">DeprecationWarning</span><span class="p">)</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="kn">import</span> <span class="nn">compiler</span>
+        <span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
+            <span class="kn">import</span> <span class="nn">ast</span> <span class="kn">as</span> <span class="nn">compiler</span>
+
+    <span class="n">walker</span> <span class="o">=</span> <span class="n">SafeEval</span><span class="p">()</span>
+    <span class="k">try</span><span class="p">:</span>
+        <span class="n">ast</span> <span class="o">=</span> <span class="n">compiler</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s">&quot;eval&quot;</span><span class="p">)</span>
+    <span class="k">except</span> <span class="ne">SyntaxError</span><span class="p">:</span>
+        <span class="k">raise</span>
+    <span class="k">try</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">walker</span><span class="o">.</span><span class="n">visit</span><span class="p">(</span><span class="n">ast</span><span class="p">)</span>
+    <span class="k">except</span> <span class="ne">SyntaxError</span><span class="p">:</span>
+        <span class="k">raise</span>
+
+<span class="c">#-----------------------------------------------------------------------------</span>
+</pre></div>
+
+          </div>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../../../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="../../../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
+    Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
+    David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
+    Lennard van der Feltz, Philip Fowler, Joseph Goose, Richard J. Gowers, Lukas Grossar,
+    Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon, Alex Nesterenko,
+    Manuel Nuno Melo, Caio S. Souza, Danny Parton, Joshua L. Phillips, Tyler Reddy,
+    Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
+    Zhuyi Xue, Carlos Yáñez S.,
+    and Oliver Beckstein.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
+    </div>
+  </body>
+</html>
\ No newline at end of file
diff --git a/package/doc/html/_sources/documentation_pages/lib/NeighborSearch.txt b/package/doc/html/_sources/documentation_pages/lib/NeighborSearch.txt
new file mode 100644
index 00000000000..967e7a13cd9
--- /dev/null
+++ b/package/doc/html/_sources/documentation_pages/lib/NeighborSearch.txt
@@ -0,0 +1,2 @@
+.. automodule:: MDAnalysis.lib.NeighborSearch
+   :members:
diff --git a/package/doc/html/_sources/documentation_pages/lib_modules.txt b/package/doc/html/_sources/documentation_pages/lib_modules.txt
index a26537c2f1b..dac4ee7ab9f 100644
--- a/package/doc/html/_sources/documentation_pages/lib_modules.txt
+++ b/package/doc/html/_sources/documentation_pages/lib_modules.txt
@@ -22,13 +22,16 @@ superposition by minimizing the RMSD.
 :mod:`MDAnalysis.lib.util` contains various file, string
 and mathematical utility functions.
 
+:mod:`MDAnalysis.lib.NeighborSearch` contains classes to do neighbor searches
+     with MDAnalysis objects.
+
 
 .. toctree::
    :maxdepth: 1
 
    ./lib/distances
    ./lib/_distances
-   ./lib/KDTree_modules
+   ./lib/NeighborSearch
    ./lib/log
    ./lib/mdamath
    ./lib/parallel
diff --git a/package/doc/html/_sources/documentation_pages/overview.txt b/package/doc/html/_sources/documentation_pages/overview.txt
index 249afd78ee4..3e2a342cda8 100644
--- a/package/doc/html/_sources/documentation_pages/overview.txt
+++ b/package/doc/html/_sources/documentation_pages/overview.txt
@@ -9,7 +9,7 @@ objects. Each object has a number of operations defined on itself
 (also known as "methods") and also contains values describing the
 object ("attributes"). For example, a
 :class:`~MDAnalysis.core.AtomGroup.AtomGroup` object has a
-:meth:`~MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass` method that
+:meth:`~MDAnalysis.core.AtomGroup.AtomGroup.center_of_mass` method that
 returns the center of mass of the group of atoms. It also contains an
 attribute called :attr:`~MDAnalysis.core.AtomGroup.AtomGroup.residues`
 that lists all the residues that belong to the group. Using methods
@@ -32,7 +32,7 @@ of a protein and the radius of gyration of the backbone atoms are calculated::
   for ts in u.trajectory:     # iterate through all frames
     r = cterm.pos - nterm.pos # end-to-end vector from atom positions
     d = numpy.linalg.norm(r)  # end-to-end distance
-    rgyr = bb.radiusOfGyration()  # method of a AtomGroup; updates with each frame
+    rgyr = bb.radius_of_gyration()  # method of a AtomGroup; updates with each frame
     print "frame = %d: d = %f Angstroem, Rgyr = %f Angstroem" % (ts.frame, d, rgyr)
 
 
diff --git a/package/doc/html/_sources/documentation_pages/visualization_modules.txt b/package/doc/html/_sources/documentation_pages/visualization_modules.txt
index 1b87221dd78..10467019e80 100644
--- a/package/doc/html/_sources/documentation_pages/visualization_modules.txt
+++ b/package/doc/html/_sources/documentation_pages/visualization_modules.txt
@@ -4,11 +4,14 @@
 Visualization modules
 *********************
 
-The MDAnalysis.visualization namespace contains code to carry out analyses which return data that is specifically-tailored for visualization.
+The MDAnalysis.visualization namespace contains code to carry out analyses
+which return data that is specifically-tailored for visualization.
 
-Please see the individual module documentation for additional references and citation information.
+Please see the individual module documentation for additional references and
+citation information.
 
-These modules are not imported by default; in order to use them one has to import them from :mod:`MDAnalysis.visualization`, for instance: ::
+These modules are not imported by default; in order to use them one has to
+import them from :mod:`MDAnalysis.visualization`, for instance: ::
 
     import MDAnalysis.visualization.streamlines
 
diff --git a/package/doc/html/_static/basic.css b/package/doc/html/_static/basic.css
index 43e8bafaf35..9fa77d886d4 100644
--- a/package/doc/html/_static/basic.css
+++ b/package/doc/html/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -89,6 +89,7 @@ div.sphinxsidebar #searchbox input[type="submit"] {
 
 img {
     border: 0;
+    max-width: 100%;
 }
 
 /* -- search page ----------------------------------------------------------- */
@@ -196,7 +197,10 @@ h3:hover > a.headerlink,
 h4:hover > a.headerlink,
 h5:hover > a.headerlink,
 h6:hover > a.headerlink,
-dt:hover > a.headerlink {
+dt:hover > a.headerlink,
+caption:hover > a.headerlink,
+p.caption:hover > a.headerlink,
+div.code-block-caption:hover > a.headerlink {
     visibility: visible;
 }
 
@@ -313,6 +317,13 @@ table.docutils {
     border-collapse: collapse;
 }
 
+table caption span.caption-number {
+    font-style: italic;
+}
+
+table caption span.caption-text {
+}
+
 table.docutils td, table.docutils th {
     padding: 1px 8px 1px 5px;
     border-top: 0;
@@ -343,6 +354,25 @@ table.citation td {
     border-bottom: none;
 }
 
+/* -- figures --------------------------------------------------------------- */
+
+div.figure {
+    margin: 0.5em;
+    padding: 0.5em;
+}
+
+div.figure p.caption {
+    padding: 0.3em;
+}
+
+div.figure p.caption span.caption-number {
+    font-style: italic;
+}
+
+div.figure p.caption span.caption-text {
+}
+
+
 /* -- other body styles ----------------------------------------------------- */
 
 ol.arabic {
@@ -401,14 +431,14 @@ dl.glossary dt {
     margin: 0;
 }
 
-.refcount {
-    color: #060;
-}
-
 .optional {
     font-size: 1.3em;
 }
 
+.sig-paren {
+    font-size: larger;
+}
+
 .versionmodified {
     font-style: italic;
 }
@@ -474,22 +504,51 @@ table.highlighttable td {
     padding: 0 0.5em 0 0.5em;
 }
 
-tt.descname {
+div.code-block-caption {
+    padding: 2px 5px;
+    font-size: small;
+}
+
+div.code-block-caption code {
+    background-color: transparent;
+}
+
+div.code-block-caption + div > div.highlight > pre {
+    margin-top: 0;
+}
+
+div.code-block-caption span.caption-number {
+    padding: 0.1em 0.3em;
+    font-style: italic;
+}
+
+div.code-block-caption span.caption-text {
+}
+
+div.literal-block-wrapper {
+    padding: 1em 1em 0;
+}
+
+div.literal-block-wrapper div.highlight {
+    margin: 0;
+}
+
+code.descname {
     background-color: transparent;
     font-weight: bold;
     font-size: 1.2em;
 }
 
-tt.descclassname {
+code.descclassname {
     background-color: transparent;
 }
 
-tt.xref, a tt {
+code.xref, a code {
     background-color: transparent;
     font-weight: bold;
 }
 
-h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt {
+h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
     background-color: transparent;
 }
 
diff --git a/package/doc/html/_static/doctools.js b/package/doc/html/_static/doctools.js
index d4619fdfb10..c7bfe760aa8 100644
--- a/package/doc/html/_static/doctools.js
+++ b/package/doc/html/_static/doctools.js
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -32,7 +32,7 @@ if (!window.console || !console.firebug) {
  */
 jQuery.urldecode = function(x) {
   return decodeURIComponent(x).replace(/\+/g, ' ');
-}
+};
 
 /**
  * small helper function to urlencode strings
@@ -61,18 +61,6 @@ jQuery.getQueryParameters = function(s) {
   return result;
 };
 
-/**
- * small function to check if an array contains
- * a given item.
- */
-jQuery.contains = function(arr, item) {
-  for (var i = 0; i < arr.length; i++) {
-    if (arr[i] == item)
-      return true;
-  }
-  return false;
-};
-
 /**
  * highlight a given string on a jquery object by wrapping it in
  * span elements with the given class name.
@@ -103,6 +91,30 @@ jQuery.fn.highlightText = function(text, className) {
   });
 };
 
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+  jQuery.uaMatch = function(ua) {
+    ua = ua.toLowerCase();
+
+    var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+      /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+      /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+      /(msie) ([\w.]+)/.exec(ua) ||
+      ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+      [];
+
+    return {
+      browser: match[ 1 ] || "",
+      version: match[ 2 ] || "0"
+    };
+  };
+  jQuery.browser = {};
+  jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}
+
 /**
  * Small JavaScript module for the documentation.
  */
@@ -164,9 +176,10 @@ var Documentation = {
 
   /**
    * workaround a firefox stupidity
+   * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
    */
   fixFirefoxAnchorBug : function() {
-    if (document.location.hash && $.browser.mozilla)
+    if (document.location.hash)
       window.setTimeout(function() {
         document.location.href += '';
       }, 10);
@@ -180,6 +193,9 @@ var Documentation = {
     var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
     if (terms.length) {
       var body = $('div.body');
+      if (!body.length) {
+        body = $('body');
+      }
       window.setTimeout(function() {
         $.each(terms, function() {
           body.highlightText(this.toLowerCase(), 'highlighted');
diff --git a/package/doc/html/_static/down-pressed.png b/package/doc/html/_static/down-pressed.png
index 6f7ad782782..7c30d004b71 100644
Binary files a/package/doc/html/_static/down-pressed.png and b/package/doc/html/_static/down-pressed.png differ
diff --git a/package/doc/html/_static/down.png b/package/doc/html/_static/down.png
index 3003a88770d..f48098a43b0 100644
Binary files a/package/doc/html/_static/down.png and b/package/doc/html/_static/down.png differ
diff --git a/package/doc/html/_static/file.png b/package/doc/html/_static/file.png
index d18082e397e..254c60bfbe2 100644
Binary files a/package/doc/html/_static/file.png and b/package/doc/html/_static/file.png differ
diff --git a/package/doc/html/_static/jquery-1.11.1.js b/package/doc/html/_static/jquery-1.11.1.js
new file mode 100644
index 00000000000..d4b67f7e6c1
--- /dev/null
+++ b/package/doc/html/_static/jquery-1.11.1.js
@@ -0,0 +1,10308 @@
+/*!
+ * jQuery JavaScript Library v1.11.1
+ * http://jquery.com/
+ *
+ * Includes Sizzle.js
+ * http://sizzlejs.com/
+ *
+ * Copyright 2005, 2014 jQuery Foundation, Inc. and other contributors
+ * Released under the MIT license
+ * http://jquery.org/license
+ *
+ * Date: 2014-05-01T17:42Z
+ */
+
+(function( global, factory ) {
+
+	if ( typeof module === "object" && typeof module.exports === "object" ) {
+		// For CommonJS and CommonJS-like environments where a proper window is present,
+		// execute the factory and get jQuery
+		// For environments that do not inherently posses a window with a document
+		// (such as Node.js), expose a jQuery-making factory as module.exports
+		// This accentuates the need for the creation of a real window
+		// e.g. var jQuery = require("jquery")(window);
+		// See ticket #14549 for more info
+		module.exports = global.document ?
+			factory( global, true ) :
+			function( w ) {
+				if ( !w.document ) {
+					throw new Error( "jQuery requires a window with a document" );
+				}
+				return factory( w );
+			};
+	} else {
+		factory( global );
+	}
+
+// Pass this if window is not defined yet
+}(typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
+
+// Can't do this because several apps including ASP.NET trace
+// the stack via arguments.caller.callee and Firefox dies if
+// you try to trace through "use strict" call chains. (#13335)
+// Support: Firefox 18+
+//
+
+var deletedIds = [];
+
+var slice = deletedIds.slice;
+
+var concat = deletedIds.concat;
+
+var push = deletedIds.push;
+
+var indexOf = deletedIds.indexOf;
+
+var class2type = {};
+
+var toString = class2type.toString;
+
+var hasOwn = class2type.hasOwnProperty;
+
+var support = {};
+
+
+
+var
+	version = "1.11.1",
+
+	// Define a local copy of jQuery
+	jQuery = function( selector, context ) {
+		// The jQuery object is actually just the init constructor 'enhanced'
+		// Need init if jQuery is called (just allow error to be thrown if not included)
+		return new jQuery.fn.init( selector, context );
+	},
+
+	// Support: Android<4.1, IE<9
+	// Make sure we trim BOM and NBSP
+	rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,
+
+	// Matches dashed string for camelizing
+	rmsPrefix = /^-ms-/,
+	rdashAlpha = /-([\da-z])/gi,
+
+	// Used by jQuery.camelCase as callback to replace()
+	fcamelCase = function( all, letter ) {
+		return letter.toUpperCase();
+	};
+
+jQuery.fn = jQuery.prototype = {
+	// The current version of jQuery being used
+	jquery: version,
+
+	constructor: jQuery,
+
+	// Start with an empty selector
+	selector: "",
+
+	// The default length of a jQuery object is 0
+	length: 0,
+
+	toArray: function() {
+		return slice.call( this );
+	},
+
+	// Get the Nth element in the matched element set OR
+	// Get the whole matched element set as a clean array
+	get: function( num ) {
+		return num != null ?
+
+			// Return just the one element from the set
+			( num < 0 ? this[ num + this.length ] : this[ num ] ) :
+
+			// Return all the elements in a clean array
+			slice.call( this );
+	},
+
+	// Take an array of elements and push it onto the stack
+	// (returning the new matched element set)
+	pushStack: function( elems ) {
+
+		// Build a new jQuery matched element set
+		var ret = jQuery.merge( this.constructor(), elems );
+
+		// Add the old object onto the stack (as a reference)
+		ret.prevObject = this;
+		ret.context = this.context;
+
+		// Return the newly-formed element set
+		return ret;
+	},
+
+	// Execute a callback for every element in the matched set.
+	// (You can seed the arguments with an array of args, but this is
+	// only used internally.)
+	each: function( callback, args ) {
+		return jQuery.each( this, callback, args );
+	},
+
+	map: function( callback ) {
+		return this.pushStack( jQuery.map(this, function( elem, i ) {
+			return callback.call( elem, i, elem );
+		}));
+	},
+
+	slice: function() {
+		return this.pushStack( slice.apply( this, arguments ) );
+	},
+
+	first: function() {
+		return this.eq( 0 );
+	},
+
+	last: function() {
+		return this.eq( -1 );
+	},
+
+	eq: function( i ) {
+		var len = this.length,
+			j = +i + ( i < 0 ? len : 0 );
+		return this.pushStack( j >= 0 && j < len ? [ this[j] ] : [] );
+	},
+
+	end: function() {
+		return this.prevObject || this.constructor(null);
+	},
+
+	// For internal use only.
+	// Behaves like an Array's method, not like a jQuery method.
+	push: push,
+	sort: deletedIds.sort,
+	splice: deletedIds.splice
+};
+
+jQuery.extend = jQuery.fn.extend = function() {
+	var src, copyIsArray, copy, name, options, clone,
+		target = arguments[0] || {},
+		i = 1,
+		length = arguments.length,
+		deep = false;
+
+	// Handle a deep copy situation
+	if ( typeof target === "boolean" ) {
+		deep = target;
+
+		// skip the boolean and the target
+		target = arguments[ i ] || {};
+		i++;
+	}
+
+	// Handle case when target is a string or something (possible in deep copy)
+	if ( typeof target !== "object" && !jQuery.isFunction(target) ) {
+		target = {};
+	}
+
+	// extend jQuery itself if only one argument is passed
+	if ( i === length ) {
+		target = this;
+		i--;
+	}
+
+	for ( ; i < length; i++ ) {
+		// Only deal with non-null/undefined values
+		if ( (options = arguments[ i ]) != null ) {
+			// Extend the base object
+			for ( name in options ) {
+				src = target[ name ];
+				copy = options[ name ];
+
+				// Prevent never-ending loop
+				if ( target === copy ) {
+					continue;
+				}
+
+				// Recurse if we're merging plain objects or arrays
+				if ( deep && copy && ( jQuery.isPlainObject(copy) || (copyIsArray = jQuery.isArray(copy)) ) ) {
+					if ( copyIsArray ) {
+						copyIsArray = false;
+						clone = src && jQuery.isArray(src) ? src : [];
+
+					} else {
+						clone = src && jQuery.isPlainObject(src) ? src : {};
+					}
+
+					// Never move original objects, clone them
+					target[ name ] = jQuery.extend( deep, clone, copy );
+
+				// Don't bring in undefined values
+				} else if ( copy !== undefined ) {
+					target[ name ] = copy;
+				}
+			}
+		}
+	}
+
+	// Return the modified object
+	return target;
+};
+
+jQuery.extend({
+	// Unique for each copy of jQuery on the page
+	expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ),
+
+	// Assume jQuery is ready without the ready module
+	isReady: true,
+
+	error: function( msg ) {
+		throw new Error( msg );
+	},
+
+	noop: function() {},
+
+	// See test/unit/core.js for details concerning isFunction.
+	// Since version 1.3, DOM methods and functions like alert
+	// aren't supported. They return false on IE (#2968).
+	isFunction: function( obj ) {
+		return jQuery.type(obj) === "function";
+	},
+
+	isArray: Array.isArray || function( obj ) {
+		return jQuery.type(obj) === "array";
+	},
+
+	isWindow: function( obj ) {
+		/* jshint eqeqeq: false */
+		return obj != null && obj == obj.window;
+	},
+
+	isNumeric: function( obj ) {
+		// parseFloat NaNs numeric-cast false positives (null|true|false|"")
+		// ...but misinterprets leading-number strings, particularly hex literals ("0x...")
+		// subtraction forces infinities to NaN
+		return !jQuery.isArray( obj ) && obj - parseFloat( obj ) >= 0;
+	},
+
+	isEmptyObject: function( obj ) {
+		var name;
+		for ( name in obj ) {
+			return false;
+		}
+		return true;
+	},
+
+	isPlainObject: function( obj ) {
+		var key;
+
+		// Must be an Object.
+		// Because of IE, we also have to check the presence of the constructor property.
+		// Make sure that DOM nodes and window objects don't pass through, as well
+		if ( !obj || jQuery.type(obj) !== "object" || obj.nodeType || jQuery.isWindow( obj ) ) {
+			return false;
+		}
+
+		try {
+			// Not own constructor property must be Object
+			if ( obj.constructor &&
+				!hasOwn.call(obj, "constructor") &&
+				!hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) {
+				return false;
+			}
+		} catch ( e ) {
+			// IE8,9 Will throw exceptions on certain host objects #9897
+			return false;
+		}
+
+		// Support: IE<9
+		// Handle iteration over inherited properties before own properties.
+		if ( support.ownLast ) {
+			for ( key in obj ) {
+				return hasOwn.call( obj, key );
+			}
+		}
+
+		// Own properties are enumerated firstly, so to speed up,
+		// if last one is own, then all properties are own.
+		for ( key in obj ) {}
+
+		return key === undefined || hasOwn.call( obj, key );
+	},
+
+	type: function( obj ) {
+		if ( obj == null ) {
+			return obj + "";
+		}
+		return typeof obj === "object" || typeof obj === "function" ?
+			class2type[ toString.call(obj) ] || "object" :
+			typeof obj;
+	},
+
+	// Evaluates a script in a global context
+	// Workarounds based on findings by Jim Driscoll
+	// http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context
+	globalEval: function( data ) {
+		if ( data && jQuery.trim( data ) ) {
+			// We use execScript on Internet Explorer
+			// We use an anonymous function so that context is window
+			// rather than jQuery in Firefox
+			( window.execScript || function( data ) {
+				window[ "eval" ].call( window, data );
+			} )( data );
+		}
+	},
+
+	// Convert dashed to camelCase; used by the css and data modules
+	// Microsoft forgot to hump their vendor prefix (#9572)
+	camelCase: function( string ) {
+		return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
+	},
+
+	nodeName: function( elem, name ) {
+		return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
+	},
+
+	// args is for internal usage only
+	each: function( obj, callback, args ) {
+		var value,
+			i = 0,
+			length = obj.length,
+			isArray = isArraylike( obj );
+
+		if ( args ) {
+			if ( isArray ) {
+				for ( ; i < length; i++ ) {
+					value = callback.apply( obj[ i ], args );
+
+					if ( value === false ) {
+						break;
+					}
+				}
+			} else {
+				for ( i in obj ) {
+					value = callback.apply( obj[ i ], args );
+
+					if ( value === false ) {
+						break;
+					}
+				}
+			}
+
+		// A special, fast, case for the most common use of each
+		} else {
+			if ( isArray ) {
+				for ( ; i < length; i++ ) {
+					value = callback.call( obj[ i ], i, obj[ i ] );
+
+					if ( value === false ) {
+						break;
+					}
+				}
+			} else {
+				for ( i in obj ) {
+					value = callback.call( obj[ i ], i, obj[ i ] );
+
+					if ( value === false ) {
+						break;
+					}
+				}
+			}
+		}
+
+		return obj;
+	},
+
+	// Support: Android<4.1, IE<9
+	trim: function( text ) {
+		return text == null ?
+			"" :
+			( text + "" ).replace( rtrim, "" );
+	},
+
+	// results is for internal usage only
+	makeArray: function( arr, results ) {
+		var ret = results || [];
+
+		if ( arr != null ) {
+			if ( isArraylike( Object(arr) ) ) {
+				jQuery.merge( ret,
+					typeof arr === "string" ?
+					[ arr ] : arr
+				);
+			} else {
+				push.call( ret, arr );
+			}
+		}
+
+		return ret;
+	},
+
+	inArray: function( elem, arr, i ) {
+		var len;
+
+		if ( arr ) {
+			if ( indexOf ) {
+				return indexOf.call( arr, elem, i );
+			}
+
+			len = arr.length;
+			i = i ? i < 0 ? Math.max( 0, len + i ) : i : 0;
+
+			for ( ; i < len; i++ ) {
+				// Skip accessing in sparse arrays
+				if ( i in arr && arr[ i ] === elem ) {
+					return i;
+				}
+			}
+		}
+
+		return -1;
+	},
+
+	merge: function( first, second ) {
+		var len = +second.length,
+			j = 0,
+			i = first.length;
+
+		while ( j < len ) {
+			first[ i++ ] = second[ j++ ];
+		}
+
+		// Support: IE<9
+		// Workaround casting of .length to NaN on otherwise arraylike objects (e.g., NodeLists)
+		if ( len !== len ) {
+			while ( second[j] !== undefined ) {
+				first[ i++ ] = second[ j++ ];
+			}
+		}
+
+		first.length = i;
+
+		return first;
+	},
+
+	grep: function( elems, callback, invert ) {
+		var callbackInverse,
+			matches = [],
+			i = 0,
+			length = elems.length,
+			callbackExpect = !invert;
+
+		// Go through the array, only saving the items
+		// that pass the validator function
+		for ( ; i < length; i++ ) {
+			callbackInverse = !callback( elems[ i ], i );
+			if ( callbackInverse !== callbackExpect ) {
+				matches.push( elems[ i ] );
+			}
+		}
+
+		return matches;
+	},
+
+	// arg is for internal usage only
+	map: function( elems, callback, arg ) {
+		var value,
+			i = 0,
+			length = elems.length,
+			isArray = isArraylike( elems ),
+			ret = [];
+
+		// Go through the array, translating each of the items to their new values
+		if ( isArray ) {
+			for ( ; i < length; i++ ) {
+				value = callback( elems[ i ], i, arg );
+
+				if ( value != null ) {
+					ret.push( value );
+				}
+			}
+
+		// Go through every key on the object,
+		} else {
+			for ( i in elems ) {
+				value = callback( elems[ i ], i, arg );
+
+				if ( value != null ) {
+					ret.push( value );
+				}
+			}
+		}
+
+		// Flatten any nested arrays
+		return concat.apply( [], ret );
+	},
+
+	// A global GUID counter for objects
+	guid: 1,
+
+	// Bind a function to a context, optionally partially applying any
+	// arguments.
+	proxy: function( fn, context ) {
+		var args, proxy, tmp;
+
+		if ( typeof context === "string" ) {
+			tmp = fn[ context ];
+			context = fn;
+			fn = tmp;
+		}
+
+		// Quick check to determine if target is callable, in the spec
+		// this throws a TypeError, but we will just return undefined.
+		if ( !jQuery.isFunction( fn ) ) {
+			return undefined;
+		}
+
+		// Simulated bind
+		args = slice.call( arguments, 2 );
+		proxy = function() {
+			return fn.apply( context || this, args.concat( slice.call( arguments ) ) );
+		};
+
+		// Set the guid of unique handler to the same of original handler, so it can be removed
+		proxy.guid = fn.guid = fn.guid || jQuery.guid++;
+
+		return proxy;
+	},
+
+	now: function() {
+		return +( new Date() );
+	},
+
+	// jQuery.support is not used in Core but other projects attach their
+	// properties to it so it needs to exist.
+	support: support
+});
+
+// Populate the class2type map
+jQuery.each("Boolean Number String Function Array Date RegExp Object Error".split(" "), function(i, name) {
+	class2type[ "[object " + name + "]" ] = name.toLowerCase();
+});
+
+function isArraylike( obj ) {
+	var length = obj.length,
+		type = jQuery.type( obj );
+
+	if ( type === "function" || jQuery.isWindow( obj ) ) {
+		return false;
+	}
+
+	if ( obj.nodeType === 1 && length ) {
+		return true;
+	}
+
+	return type === "array" || length === 0 ||
+		typeof length === "number" && length > 0 && ( length - 1 ) in obj;
+}
+var Sizzle =
+/*!
+ * Sizzle CSS Selector Engine v1.10.19
+ * http://sizzlejs.com/
+ *
+ * Copyright 2013 jQuery Foundation, Inc. and other contributors
+ * Released under the MIT license
+ * http://jquery.org/license
+ *
+ * Date: 2014-04-18
+ */
+(function( window ) {
+
+var i,
+	support,
+	Expr,
+	getText,
+	isXML,
+	tokenize,
+	compile,
+	select,
+	outermostContext,
+	sortInput,
+	hasDuplicate,
+
+	// Local document vars
+	setDocument,
+	document,
+	docElem,
+	documentIsHTML,
+	rbuggyQSA,
+	rbuggyMatches,
+	matches,
+	contains,
+
+	// Instance-specific data
+	expando = "sizzle" + -(new Date()),
+	preferredDoc = window.document,
+	dirruns = 0,
+	done = 0,
+	classCache = createCache(),
+	tokenCache = createCache(),
+	compilerCache = createCache(),
+	sortOrder = function( a, b ) {
+		if ( a === b ) {
+			hasDuplicate = true;
+		}
+		return 0;
+	},
+
+	// General-purpose constants
+	strundefined = typeof undefined,
+	MAX_NEGATIVE = 1 << 31,
+
+	// Instance methods
+	hasOwn = ({}).hasOwnProperty,
+	arr = [],
+	pop = arr.pop,
+	push_native = arr.push,
+	push = arr.push,
+	slice = arr.slice,
+	// Use a stripped-down indexOf if we can't use a native one
+	indexOf = arr.indexOf || function( elem ) {
+		var i = 0,
+			len = this.length;
+		for ( ; i < len; i++ ) {
+			if ( this[i] === elem ) {
+				return i;
+			}
+		}
+		return -1;
+	},
+
+	booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped",
+
+	// Regular expressions
+
+	// Whitespace characters http://www.w3.org/TR/css3-selectors/#whitespace
+	whitespace = "[\\x20\\t\\r\\n\\f]",
+	// http://www.w3.org/TR/css3-syntax/#characters
+	characterEncoding = "(?:\\\\.|[\\w-]|[^\\x00-\\xa0])+",
+
+	// Loosely modeled on CSS identifier characters
+	// An unquoted value should be a CSS identifier http://www.w3.org/TR/css3-selectors/#attribute-selectors
+	// Proper syntax: http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
+	identifier = characterEncoding.replace( "w", "w#" ),
+
+	// Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors
+	attributes = "\\[" + whitespace + "*(" + characterEncoding + ")(?:" + whitespace +
+		// Operator (capture 2)
+		"*([*^$|!~]?=)" + whitespace +
+		// "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]"
+		"*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace +
+		"*\\]",
+
+	pseudos = ":(" + characterEncoding + ")(?:\\((" +
+		// To reduce the number of selectors needing tokenize in the preFilter, prefer arguments:
+		// 1. quoted (capture 3; capture 4 or capture 5)
+		"('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" +
+		// 2. simple (capture 6)
+		"((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" +
+		// 3. anything else (capture 2)
+		".*" +
+		")\\)|)",
+
+	// Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
+	rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ),
+
+	rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
+	rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ),
+
+	rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ),
+
+	rpseudo = new RegExp( pseudos ),
+	ridentifier = new RegExp( "^" + identifier + "$" ),
+
+	matchExpr = {
+		"ID": new RegExp( "^#(" + characterEncoding + ")" ),
+		"CLASS": new RegExp( "^\\.(" + characterEncoding + ")" ),
+		"TAG": new RegExp( "^(" + characterEncoding.replace( "w", "w*" ) + ")" ),
+		"ATTR": new RegExp( "^" + attributes ),
+		"PSEUDO": new RegExp( "^" + pseudos ),
+		"CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace +
+			"*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace +
+			"*(\\d+)|))" + whitespace + "*\\)|)", "i" ),
+		"bool": new RegExp( "^(?:" + booleans + ")$", "i" ),
+		// For use in libraries implementing .is()
+		// We use this for POS matching in `select`
+		"needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" +
+			whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" )
+	},
+
+	rinputs = /^(?:input|select|textarea|button)$/i,
+	rheader = /^h\d$/i,
+
+	rnative = /^[^{]+\{\s*\[native \w/,
+
+	// Easily-parseable/retrievable ID or TAG or CLASS selectors
+	rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,
+
+	rsibling = /[+~]/,
+	rescape = /'|\\/g,
+
+	// CSS escapes http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
+	runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ),
+	funescape = function( _, escaped, escapedWhitespace ) {
+		var high = "0x" + escaped - 0x10000;
+		// NaN means non-codepoint
+		// Support: Firefox<24
+		// Workaround erroneous numeric interpretation of +"0x"
+		return high !== high || escapedWhitespace ?
+			escaped :
+			high < 0 ?
+				// BMP codepoint
+				String.fromCharCode( high + 0x10000 ) :
+				// Supplemental Plane codepoint (surrogate pair)
+				String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );
+	};
+
+// Optimize for push.apply( _, NodeList )
+try {
+	push.apply(
+		(arr = slice.call( preferredDoc.childNodes )),
+		preferredDoc.childNodes
+	);
+	// Support: Android<4.0
+	// Detect silently failing push.apply
+	arr[ preferredDoc.childNodes.length ].nodeType;
+} catch ( e ) {
+	push = { apply: arr.length ?
+
+		// Leverage slice if possible
+		function( target, els ) {
+			push_native.apply( target, slice.call(els) );
+		} :
+
+		// Support: IE<9
+		// Otherwise append directly
+		function( target, els ) {
+			var j = target.length,
+				i = 0;
+			// Can't trust NodeList.length
+			while ( (target[j++] = els[i++]) ) {}
+			target.length = j - 1;
+		}
+	};
+}
+
+function Sizzle( selector, context, results, seed ) {
+	var match, elem, m, nodeType,
+		// QSA vars
+		i, groups, old, nid, newContext, newSelector;
+
+	if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {
+		setDocument( context );
+	}
+
+	context = context || document;
+	results = results || [];
+
+	if ( !selector || typeof selector !== "string" ) {
+		return results;
+	}
+
+	if ( (nodeType = context.nodeType) !== 1 && nodeType !== 9 ) {
+		return [];
+	}
+
+	if ( documentIsHTML && !seed ) {
+
+		// Shortcuts
+		if ( (match = rquickExpr.exec( selector )) ) {
+			// Speed-up: Sizzle("#ID")
+			if ( (m = match[1]) ) {
+				if ( nodeType === 9 ) {
+					elem = context.getElementById( m );
+					// Check parentNode to catch when Blackberry 4.6 returns
+					// nodes that are no longer in the document (jQuery #6963)
+					if ( elem && elem.parentNode ) {
+						// Handle the case where IE, Opera, and Webkit return items
+						// by name instead of ID
+						if ( elem.id === m ) {
+							results.push( elem );
+							return results;
+						}
+					} else {
+						return results;
+					}
+				} else {
+					// Context is not a document
+					if ( context.ownerDocument && (elem = context.ownerDocument.getElementById( m )) &&
+						contains( context, elem ) && elem.id === m ) {
+						results.push( elem );
+						return results;
+					}
+				}
+
+			// Speed-up: Sizzle("TAG")
+			} else if ( match[2] ) {
+				push.apply( results, context.getElementsByTagName( selector ) );
+				return results;
+
+			// Speed-up: Sizzle(".CLASS")
+			} else if ( (m = match[3]) && support.getElementsByClassName && context.getElementsByClassName ) {
+				push.apply( results, context.getElementsByClassName( m ) );
+				return results;
+			}
+		}
+
+		// QSA path
+		if ( support.qsa && (!rbuggyQSA || !rbuggyQSA.test( selector )) ) {
+			nid = old = expando;
+			newContext = context;
+			newSelector = nodeType === 9 && selector;
+
+			// qSA works strangely on Element-rooted queries
+			// We can work around this by specifying an extra ID on the root
+			// and working up from there (Thanks to Andrew Dupont for the technique)
+			// IE 8 doesn't work on object elements
+			if ( nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) {
+				groups = tokenize( selector );
+
+				if ( (old = context.getAttribute("id")) ) {
+					nid = old.replace( rescape, "\\$&" );
+				} else {
+					context.setAttribute( "id", nid );
+				}
+				nid = "[id='" + nid + "'] ";
+
+				i = groups.length;
+				while ( i-- ) {
+					groups[i] = nid + toSelector( groups[i] );
+				}
+				newContext = rsibling.test( selector ) && testContext( context.parentNode ) || context;
+				newSelector = groups.join(",");
+			}
+
+			if ( newSelector ) {
+				try {
+					push.apply( results,
+						newContext.querySelectorAll( newSelector )
+					);
+					return results;
+				} catch(qsaError) {
+				} finally {
+					if ( !old ) {
+						context.removeAttribute("id");
+					}
+				}
+			}
+		}
+	}
+
+	// All others
+	return select( selector.replace( rtrim, "$1" ), context, results, seed );
+}
+
+/**
+ * Create key-value caches of limited size
+ * @returns {Function(string, Object)} Returns the Object data after storing it on itself with
+ *	property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)
+ *	deleting the oldest entry
+ */
+function createCache() {
+	var keys = [];
+
+	function cache( key, value ) {
+		// Use (key + " ") to avoid collision with native prototype properties (see Issue #157)
+		if ( keys.push( key + " " ) > Expr.cacheLength ) {
+			// Only keep the most recent entries
+			delete cache[ keys.shift() ];
+		}
+		return (cache[ key + " " ] = value);
+	}
+	return cache;
+}
+
+/**
+ * Mark a function for special use by Sizzle
+ * @param {Function} fn The function to mark
+ */
+function markFunction( fn ) {
+	fn[ expando ] = true;
+	return fn;
+}
+
+/**
+ * Support testing using an element
+ * @param {Function} fn Passed the created div and expects a boolean result
+ */
+function assert( fn ) {
+	var div = document.createElement("div");
+
+	try {
+		return !!fn( div );
+	} catch (e) {
+		return false;
+	} finally {
+		// Remove from its parent by default
+		if ( div.parentNode ) {
+			div.parentNode.removeChild( div );
+		}
+		// release memory in IE
+		div = null;
+	}
+}
+
+/**
+ * Adds the same handler for all of the specified attrs
+ * @param {String} attrs Pipe-separated list of attributes
+ * @param {Function} handler The method that will be applied
+ */
+function addHandle( attrs, handler ) {
+	var arr = attrs.split("|"),
+		i = attrs.length;
+
+	while ( i-- ) {
+		Expr.attrHandle[ arr[i] ] = handler;
+	}
+}
+
+/**
+ * Checks document order of two siblings
+ * @param {Element} a
+ * @param {Element} b
+ * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b
+ */
+function siblingCheck( a, b ) {
+	var cur = b && a,
+		diff = cur && a.nodeType === 1 && b.nodeType === 1 &&
+			( ~b.sourceIndex || MAX_NEGATIVE ) -
+			( ~a.sourceIndex || MAX_NEGATIVE );
+
+	// Use IE sourceIndex if available on both nodes
+	if ( diff ) {
+		return diff;
+	}
+
+	// Check if b follows a
+	if ( cur ) {
+		while ( (cur = cur.nextSibling) ) {
+			if ( cur === b ) {
+				return -1;
+			}
+		}
+	}
+
+	return a ? 1 : -1;
+}
+
+/**
+ * Returns a function to use in pseudos for input types
+ * @param {String} type
+ */
+function createInputPseudo( type ) {
+	return function( elem ) {
+		var name = elem.nodeName.toLowerCase();
+		return name === "input" && elem.type === type;
+	};
+}
+
+/**
+ * Returns a function to use in pseudos for buttons
+ * @param {String} type
+ */
+function createButtonPseudo( type ) {
+	return function( elem ) {
+		var name = elem.nodeName.toLowerCase();
+		return (name === "input" || name === "button") && elem.type === type;
+	};
+}
+
+/**
+ * Returns a function to use in pseudos for positionals
+ * @param {Function} fn
+ */
+function createPositionalPseudo( fn ) {
+	return markFunction(function( argument ) {
+		argument = +argument;
+		return markFunction(function( seed, matches ) {
+			var j,
+				matchIndexes = fn( [], seed.length, argument ),
+				i = matchIndexes.length;
+
+			// Match elements found at the specified indexes
+			while ( i-- ) {
+				if ( seed[ (j = matchIndexes[i]) ] ) {
+					seed[j] = !(matches[j] = seed[j]);
+				}
+			}
+		});
+	});
+}
+
+/**
+ * Checks a node for validity as a Sizzle context
+ * @param {Element|Object=} context
+ * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value
+ */
+function testContext( context ) {
+	return context && typeof context.getElementsByTagName !== strundefined && context;
+}
+
+// Expose support vars for convenience
+support = Sizzle.support = {};
+
+/**
+ * Detects XML nodes
+ * @param {Element|Object} elem An element or a document
+ * @returns {Boolean} True iff elem is a non-HTML XML node
+ */
+isXML = Sizzle.isXML = function( elem ) {
+	// documentElement is verified for cases where it doesn't yet exist
+	// (such as loading iframes in IE - #4833)
+	var documentElement = elem && (elem.ownerDocument || elem).documentElement;
+	return documentElement ? documentElement.nodeName !== "HTML" : false;
+};
+
+/**
+ * Sets document-related variables once based on the current document
+ * @param {Element|Object} [doc] An element or document object to use to set the document
+ * @returns {Object} Returns the current document
+ */
+setDocument = Sizzle.setDocument = function( node ) {
+	var hasCompare,
+		doc = node ? node.ownerDocument || node : preferredDoc,
+		parent = doc.defaultView;
+
+	// If no document and documentElement is available, return
+	if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) {
+		return document;
+	}
+
+	// Set our document
+	document = doc;
+	docElem = doc.documentElement;
+
+	// Support tests
+	documentIsHTML = !isXML( doc );
+
+	// Support: IE>8
+	// If iframe document is assigned to "document" variable and if iframe has been reloaded,
+	// IE will throw "permission denied" error when accessing "document" variable, see jQuery #13936
+	// IE6-8 do not support the defaultView property so parent will be undefined
+	if ( parent && parent !== parent.top ) {
+		// IE11 does not have attachEvent, so all must suffer
+		if ( parent.addEventListener ) {
+			parent.addEventListener( "unload", function() {
+				setDocument();
+			}, false );
+		} else if ( parent.attachEvent ) {
+			parent.attachEvent( "onunload", function() {
+				setDocument();
+			});
+		}
+	}
+
+	/* Attributes
+	---------------------------------------------------------------------- */
+
+	// Support: IE<8
+	// Verify that getAttribute really returns attributes and not properties (excepting IE8 booleans)
+	support.attributes = assert(function( div ) {
+		div.className = "i";
+		return !div.getAttribute("className");
+	});
+
+	/* getElement(s)By*
+	---------------------------------------------------------------------- */
+
+	// Check if getElementsByTagName("*") returns only elements
+	support.getElementsByTagName = assert(function( div ) {
+		div.appendChild( doc.createComment("") );
+		return !div.getElementsByTagName("*").length;
+	});
+
+	// Check if getElementsByClassName can be trusted
+	support.getElementsByClassName = rnative.test( doc.getElementsByClassName ) && assert(function( div ) {
+		div.innerHTML = "<div class='a'></div><div class='a i'></div>";
+
+		// Support: Safari<4
+		// Catch class over-caching
+		div.firstChild.className = "i";
+		// Support: Opera<10
+		// Catch gEBCN failure to find non-leading classes
+		return div.getElementsByClassName("i").length === 2;
+	});
+
+	// Support: IE<10
+	// Check if getElementById returns elements by name
+	// The broken getElementById methods don't pick up programatically-set names,
+	// so use a roundabout getElementsByName test
+	support.getById = assert(function( div ) {
+		docElem.appendChild( div ).id = expando;
+		return !doc.getElementsByName || !doc.getElementsByName( expando ).length;
+	});
+
+	// ID find and filter
+	if ( support.getById ) {
+		Expr.find["ID"] = function( id, context ) {
+			if ( typeof context.getElementById !== strundefined && documentIsHTML ) {
+				var m = context.getElementById( id );
+				// Check parentNode to catch when Blackberry 4.6 returns
+				// nodes that are no longer in the document #6963
+				return m && m.parentNode ? [ m ] : [];
+			}
+		};
+		Expr.filter["ID"] = function( id ) {
+			var attrId = id.replace( runescape, funescape );
+			return function( elem ) {
+				return elem.getAttribute("id") === attrId;
+			};
+		};
+	} else {
+		// Support: IE6/7
+		// getElementById is not reliable as a find shortcut
+		delete Expr.find["ID"];
+
+		Expr.filter["ID"] =  function( id ) {
+			var attrId = id.replace( runescape, funescape );
+			return function( elem ) {
+				var node = typeof elem.getAttributeNode !== strundefined && elem.getAttributeNode("id");
+				return node && node.value === attrId;
+			};
+		};
+	}
+
+	// Tag
+	Expr.find["TAG"] = support.getElementsByTagName ?
+		function( tag, context ) {
+			if ( typeof context.getElementsByTagName !== strundefined ) {
+				return context.getElementsByTagName( tag );
+			}
+		} :
+		function( tag, context ) {
+			var elem,
+				tmp = [],
+				i = 0,
+				results = context.getElementsByTagName( tag );
+
+			// Filter out possible comments
+			if ( tag === "*" ) {
+				while ( (elem = results[i++]) ) {
+					if ( elem.nodeType === 1 ) {
+						tmp.push( elem );
+					}
+				}
+
+				return tmp;
+			}
+			return results;
+		};
+
+	// Class
+	Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) {
+		if ( typeof context.getElementsByClassName !== strundefined && documentIsHTML ) {
+			return context.getElementsByClassName( className );
+		}
+	};
+
+	/* QSA/matchesSelector
+	---------------------------------------------------------------------- */
+
+	// QSA and matchesSelector support
+
+	// matchesSelector(:active) reports false when true (IE9/Opera 11.5)
+	rbuggyMatches = [];
+
+	// qSa(:focus) reports false when true (Chrome 21)
+	// We allow this because of a bug in IE8/9 that throws an error
+	// whenever `document.activeElement` is accessed on an iframe
+	// So, we allow :focus to pass through QSA all the time to avoid the IE error
+	// See http://bugs.jquery.com/ticket/13378
+	rbuggyQSA = [];
+
+	if ( (support.qsa = rnative.test( doc.querySelectorAll )) ) {
+		// Build QSA regex
+		// Regex strategy adopted from Diego Perini
+		assert(function( div ) {
+			// Select is set to empty string on purpose
+			// This is to test IE's treatment of not explicitly
+			// setting a boolean content attribute,
+			// since its presence should be enough
+			// http://bugs.jquery.com/ticket/12359
+			div.innerHTML = "<select msallowclip=''><option selected=''></option></select>";
+
+			// Support: IE8, Opera 11-12.16
+			// Nothing should be selected when empty strings follow ^= or $= or *=
+			// The test attribute must be unknown in Opera but "safe" for WinRT
+			// http://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
+			if ( div.querySelectorAll("[msallowclip^='']").length ) {
+				rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" );
+			}
+
+			// Support: IE8
+			// Boolean attributes and "value" are not treated correctly
+			if ( !div.querySelectorAll("[selected]").length ) {
+				rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" );
+			}
+
+			// Webkit/Opera - :checked should return selected option elements
+			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+			// IE8 throws error here and will not see later tests
+			if ( !div.querySelectorAll(":checked").length ) {
+				rbuggyQSA.push(":checked");
+			}
+		});
+
+		assert(function( div ) {
+			// Support: Windows 8 Native Apps
+			// The type and name attributes are restricted during .innerHTML assignment
+			var input = doc.createElement("input");
+			input.setAttribute( "type", "hidden" );
+			div.appendChild( input ).setAttribute( "name", "D" );
+
+			// Support: IE8
+			// Enforce case-sensitivity of name attribute
+			if ( div.querySelectorAll("[name=d]").length ) {
+				rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" );
+			}
+
+			// FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)
+			// IE8 throws error here and will not see later tests
+			if ( !div.querySelectorAll(":enabled").length ) {
+				rbuggyQSA.push( ":enabled", ":disabled" );
+			}
+
+			// Opera 10-11 does not throw on post-comma invalid pseudos
+			div.querySelectorAll("*,:x");
+			rbuggyQSA.push(",.*:");
+		});
+	}
+
+	if ( (support.matchesSelector = rnative.test( (matches = docElem.matches ||
+		docElem.webkitMatchesSelector ||
+		docElem.mozMatchesSelector ||
+		docElem.oMatchesSelector ||
+		docElem.msMatchesSelector) )) ) {
+
+		assert(function( div ) {
+			// Check to see if it's possible to do matchesSelector
+			// on a disconnected node (IE 9)
+			support.disconnectedMatch = matches.call( div, "div" );
+
+			// This should fail with an exception
+			// Gecko does not error, returns false instead
+			matches.call( div, "[s!='']:x" );
+			rbuggyMatches.push( "!=", pseudos );
+		});
+	}
+
+	rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join("|") );
+	rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join("|") );
+
+	/* Contains
+	---------------------------------------------------------------------- */
+	hasCompare = rnative.test( docElem.compareDocumentPosition );
+
+	// Element contains another
+	// Purposefully does not implement inclusive descendent
+	// As in, an element does not contain itself
+	contains = hasCompare || rnative.test( docElem.contains ) ?
+		function( a, b ) {
+			var adown = a.nodeType === 9 ? a.documentElement : a,
+				bup = b && b.parentNode;
+			return a === bup || !!( bup && bup.nodeType === 1 && (
+				adown.contains ?
+					adown.contains( bup ) :
+					a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16
+			));
+		} :
+		function( a, b ) {
+			if ( b ) {
+				while ( (b = b.parentNode) ) {
+					if ( b === a ) {
+						return true;
+					}
+				}
+			}
+			return false;
+		};
+
+	/* Sorting
+	---------------------------------------------------------------------- */
+
+	// Document order sorting
+	sortOrder = hasCompare ?
+	function( a, b ) {
+
+		// Flag for duplicate removal
+		if ( a === b ) {
+			hasDuplicate = true;
+			return 0;
+		}
+
+		// Sort on method existence if only one input has compareDocumentPosition
+		var compare = !a.compareDocumentPosition - !b.compareDocumentPosition;
+		if ( compare ) {
+			return compare;
+		}
+
+		// Calculate position if both inputs belong to the same document
+		compare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ?
+			a.compareDocumentPosition( b ) :
+
+			// Otherwise we know they are disconnected
+			1;
+
+		// Disconnected nodes
+		if ( compare & 1 ||
+			(!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) {
+
+			// Choose the first element that is related to our preferred document
+			if ( a === doc || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) {
+				return -1;
+			}
+			if ( b === doc || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) {
+				return 1;
+			}
+
+			// Maintain original order
+			return sortInput ?
+				( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) :
+				0;
+		}
+
+		return compare & 4 ? -1 : 1;
+	} :
+	function( a, b ) {
+		// Exit early if the nodes are identical
+		if ( a === b ) {
+			hasDuplicate = true;
+			return 0;
+		}
+
+		var cur,
+			i = 0,
+			aup = a.parentNode,
+			bup = b.parentNode,
+			ap = [ a ],
+			bp = [ b ];
+
+		// Parentless nodes are either documents or disconnected
+		if ( !aup || !bup ) {
+			return a === doc ? -1 :
+				b === doc ? 1 :
+				aup ? -1 :
+				bup ? 1 :
+				sortInput ?
+				( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) :
+				0;
+
+		// If the nodes are siblings, we can do a quick check
+		} else if ( aup === bup ) {
+			return siblingCheck( a, b );
+		}
+
+		// Otherwise we need full lists of their ancestors for comparison
+		cur = a;
+		while ( (cur = cur.parentNode) ) {
+			ap.unshift( cur );
+		}
+		cur = b;
+		while ( (cur = cur.parentNode) ) {
+			bp.unshift( cur );
+		}
+
+		// Walk down the tree looking for a discrepancy
+		while ( ap[i] === bp[i] ) {
+			i++;
+		}
+
+		return i ?
+			// Do a sibling check if the nodes have a common ancestor
+			siblingCheck( ap[i], bp[i] ) :
+
+			// Otherwise nodes in our document sort first
+			ap[i] === preferredDoc ? -1 :
+			bp[i] === preferredDoc ? 1 :
+			0;
+	};
+
+	return doc;
+};
+
+Sizzle.matches = function( expr, elements ) {
+	return Sizzle( expr, null, null, elements );
+};
+
+Sizzle.matchesSelector = function( elem, expr ) {
+	// Set document vars if needed
+	if ( ( elem.ownerDocument || elem ) !== document ) {
+		setDocument( elem );
+	}
+
+	// Make sure that attribute selectors are quoted
+	expr = expr.replace( rattributeQuotes, "='$1']" );
+
+	if ( support.matchesSelector && documentIsHTML &&
+		( !rbuggyMatches || !rbuggyMatches.test( expr ) ) &&
+		( !rbuggyQSA     || !rbuggyQSA.test( expr ) ) ) {
+
+		try {
+			var ret = matches.call( elem, expr );
+
+			// IE 9's matchesSelector returns false on disconnected nodes
+			if ( ret || support.disconnectedMatch ||
+					// As well, disconnected nodes are said to be in a document
+					// fragment in IE 9
+					elem.document && elem.document.nodeType !== 11 ) {
+				return ret;
+			}
+		} catch(e) {}
+	}
+
+	return Sizzle( expr, document, null, [ elem ] ).length > 0;
+};
+
+Sizzle.contains = function( context, elem ) {
+	// Set document vars if needed
+	if ( ( context.ownerDocument || context ) !== document ) {
+		setDocument( context );
+	}
+	return contains( context, elem );
+};
+
+Sizzle.attr = function( elem, name ) {
+	// Set document vars if needed
+	if ( ( elem.ownerDocument || elem ) !== document ) {
+		setDocument( elem );
+	}
+
+	var fn = Expr.attrHandle[ name.toLowerCase() ],
+		// Don't get fooled by Object.prototype properties (jQuery #13807)
+		val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ?
+			fn( elem, name, !documentIsHTML ) :
+			undefined;
+
+	return val !== undefined ?
+		val :
+		support.attributes || !documentIsHTML ?
+			elem.getAttribute( name ) :
+			(val = elem.getAttributeNode(name)) && val.specified ?
+				val.value :
+				null;
+};
+
+Sizzle.error = function( msg ) {
+	throw new Error( "Syntax error, unrecognized expression: " + msg );
+};
+
+/**
+ * Document sorting and removing duplicates
+ * @param {ArrayLike} results
+ */
+Sizzle.uniqueSort = function( results ) {
+	var elem,
+		duplicates = [],
+		j = 0,
+		i = 0;
+
+	// Unless we *know* we can detect duplicates, assume their presence
+	hasDuplicate = !support.detectDuplicates;
+	sortInput = !support.sortStable && results.slice( 0 );
+	results.sort( sortOrder );
+
+	if ( hasDuplicate ) {
+		while ( (elem = results[i++]) ) {
+			if ( elem === results[ i ] ) {
+				j = duplicates.push( i );
+			}
+		}
+		while ( j-- ) {
+			results.splice( duplicates[ j ], 1 );
+		}
+	}
+
+	// Clear input after sorting to release objects
+	// See https://github.com/jquery/sizzle/pull/225
+	sortInput = null;
+
+	return results;
+};
+
+/**
+ * Utility function for retrieving the text value of an array of DOM nodes
+ * @param {Array|Element} elem
+ */
+getText = Sizzle.getText = function( elem ) {
+	var node,
+		ret = "",
+		i = 0,
+		nodeType = elem.nodeType;
+
+	if ( !nodeType ) {
+		// If no nodeType, this is expected to be an array
+		while ( (node = elem[i++]) ) {
+			// Do not traverse comment nodes
+			ret += getText( node );
+		}
+	} else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {
+		// Use textContent for elements
+		// innerText usage removed for consistency of new lines (jQuery #11153)
+		if ( typeof elem.textContent === "string" ) {
+			return elem.textContent;
+		} else {
+			// Traverse its children
+			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
+				ret += getText( elem );
+			}
+		}
+	} else if ( nodeType === 3 || nodeType === 4 ) {
+		return elem.nodeValue;
+	}
+	// Do not include comment or processing instruction nodes
+
+	return ret;
+};
+
+Expr = Sizzle.selectors = {
+
+	// Can be adjusted by the user
+	cacheLength: 50,
+
+	createPseudo: markFunction,
+
+	match: matchExpr,
+
+	attrHandle: {},
+
+	find: {},
+
+	relative: {
+		">": { dir: "parentNode", first: true },
+		" ": { dir: "parentNode" },
+		"+": { dir: "previousSibling", first: true },
+		"~": { dir: "previousSibling" }
+	},
+
+	preFilter: {
+		"ATTR": function( match ) {
+			match[1] = match[1].replace( runescape, funescape );
+
+			// Move the given value to match[3] whether quoted or unquoted
+			match[3] = ( match[3] || match[4] || match[5] || "" ).replace( runescape, funescape );
+
+			if ( match[2] === "~=" ) {
+				match[3] = " " + match[3] + " ";
+			}
+
+			return match.slice( 0, 4 );
+		},
+
+		"CHILD": function( match ) {
+			/* matches from matchExpr["CHILD"]
+				1 type (only|nth|...)
+				2 what (child|of-type)
+				3 argument (even|odd|\d*|\d*n([+-]\d+)?|...)
+				4 xn-component of xn+y argument ([+-]?\d*n|)
+				5 sign of xn-component
+				6 x of xn-component
+				7 sign of y-component
+				8 y of y-component
+			*/
+			match[1] = match[1].toLowerCase();
+
+			if ( match[1].slice( 0, 3 ) === "nth" ) {
+				// nth-* requires argument
+				if ( !match[3] ) {
+					Sizzle.error( match[0] );
+				}
+
+				// numeric x and y parameters for Expr.filter.CHILD
+				// remember that false/true cast respectively to 0/1
+				match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) );
+				match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" );
+
+			// other types prohibit arguments
+			} else if ( match[3] ) {
+				Sizzle.error( match[0] );
+			}
+
+			return match;
+		},
+
+		"PSEUDO": function( match ) {
+			var excess,
+				unquoted = !match[6] && match[2];
+
+			if ( matchExpr["CHILD"].test( match[0] ) ) {
+				return null;
+			}
+
+			// Accept quoted arguments as-is
+			if ( match[3] ) {
+				match[2] = match[4] || match[5] || "";
+
+			// Strip excess characters from unquoted arguments
+			} else if ( unquoted && rpseudo.test( unquoted ) &&
+				// Get excess from tokenize (recursively)
+				(excess = tokenize( unquoted, true )) &&
+				// advance to the next closing parenthesis
+				(excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) {
+
+				// excess is a negative index
+				match[0] = match[0].slice( 0, excess );
+				match[2] = unquoted.slice( 0, excess );
+			}
+
+			// Return only captures needed by the pseudo filter method (type and argument)
+			return match.slice( 0, 3 );
+		}
+	},
+
+	filter: {
+
+		"TAG": function( nodeNameSelector ) {
+			var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase();
+			return nodeNameSelector === "*" ?
+				function() { return true; } :
+				function( elem ) {
+					return elem.nodeName && elem.nodeName.toLowerCase() === nodeName;
+				};
+		},
+
+		"CLASS": function( className ) {
+			var pattern = classCache[ className + " " ];
+
+			return pattern ||
+				(pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) &&
+				classCache( className, function( elem ) {
+					return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== strundefined && elem.getAttribute("class") || "" );
+				});
+		},
+
+		"ATTR": function( name, operator, check ) {
+			return function( elem ) {
+				var result = Sizzle.attr( elem, name );
+
+				if ( result == null ) {
+					return operator === "!=";
+				}
+				if ( !operator ) {
+					return true;
+				}
+
+				result += "";
+
+				return operator === "=" ? result === check :
+					operator === "!=" ? result !== check :
+					operator === "^=" ? check && result.indexOf( check ) === 0 :
+					operator === "*=" ? check && result.indexOf( check ) > -1 :
+					operator === "$=" ? check && result.slice( -check.length ) === check :
+					operator === "~=" ? ( " " + result + " " ).indexOf( check ) > -1 :
+					operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" :
+					false;
+			};
+		},
+
+		"CHILD": function( type, what, argument, first, last ) {
+			var simple = type.slice( 0, 3 ) !== "nth",
+				forward = type.slice( -4 ) !== "last",
+				ofType = what === "of-type";
+
+			return first === 1 && last === 0 ?
+
+				// Shortcut for :nth-*(n)
+				function( elem ) {
+					return !!elem.parentNode;
+				} :
+
+				function( elem, context, xml ) {
+					var cache, outerCache, node, diff, nodeIndex, start,
+						dir = simple !== forward ? "nextSibling" : "previousSibling",
+						parent = elem.parentNode,
+						name = ofType && elem.nodeName.toLowerCase(),
+						useCache = !xml && !ofType;
+
+					if ( parent ) {
+
+						// :(first|last|only)-(child|of-type)
+						if ( simple ) {
+							while ( dir ) {
+								node = elem;
+								while ( (node = node[ dir ]) ) {
+									if ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) {
+										return false;
+									}
+								}
+								// Reverse direction for :only-* (if we haven't yet done so)
+								start = dir = type === "only" && !start && "nextSibling";
+							}
+							return true;
+						}
+
+						start = [ forward ? parent.firstChild : parent.lastChild ];
+
+						// non-xml :nth-child(...) stores cache data on `parent`
+						if ( forward && useCache ) {
+							// Seek `elem` from a previously-cached index
+							outerCache = parent[ expando ] || (parent[ expando ] = {});
+							cache = outerCache[ type ] || [];
+							nodeIndex = cache[0] === dirruns && cache[1];
+							diff = cache[0] === dirruns && cache[2];
+							node = nodeIndex && parent.childNodes[ nodeIndex ];
+
+							while ( (node = ++nodeIndex && node && node[ dir ] ||
+
+								// Fallback to seeking `elem` from the start
+								(diff = nodeIndex = 0) || start.pop()) ) {
+
+								// When found, cache indexes on `parent` and break
+								if ( node.nodeType === 1 && ++diff && node === elem ) {
+									outerCache[ type ] = [ dirruns, nodeIndex, diff ];
+									break;
+								}
+							}
+
+						// Use previously-cached element index if available
+						} else if ( useCache && (cache = (elem[ expando ] || (elem[ expando ] = {}))[ type ]) && cache[0] === dirruns ) {
+							diff = cache[1];
+
+						// xml :nth-child(...) or :nth-last-child(...) or :nth(-last)?-of-type(...)
+						} else {
+							// Use the same loop as above to seek `elem` from the start
+							while ( (node = ++nodeIndex && node && node[ dir ] ||
+								(diff = nodeIndex = 0) || start.pop()) ) {
+
+								if ( ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) && ++diff ) {
+									// Cache the index of each encountered element
+									if ( useCache ) {
+										(node[ expando ] || (node[ expando ] = {}))[ type ] = [ dirruns, diff ];
+									}
+
+									if ( node === elem ) {
+										break;
+									}
+								}
+							}
+						}
+
+						// Incorporate the offset, then check against cycle size
+						diff -= last;
+						return diff === first || ( diff % first === 0 && diff / first >= 0 );
+					}
+				};
+		},
+
+		"PSEUDO": function( pseudo, argument ) {
+			// pseudo-class names are case-insensitive
+			// http://www.w3.org/TR/selectors/#pseudo-classes
+			// Prioritize by case sensitivity in case custom pseudos are added with uppercase letters
+			// Remember that setFilters inherits from pseudos
+			var args,
+				fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] ||
+					Sizzle.error( "unsupported pseudo: " + pseudo );
+
+			// The user may use createPseudo to indicate that
+			// arguments are needed to create the filter function
+			// just as Sizzle does
+			if ( fn[ expando ] ) {
+				return fn( argument );
+			}
+
+			// But maintain support for old signatures
+			if ( fn.length > 1 ) {
+				args = [ pseudo, pseudo, "", argument ];
+				return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ?
+					markFunction(function( seed, matches ) {
+						var idx,
+							matched = fn( seed, argument ),
+							i = matched.length;
+						while ( i-- ) {
+							idx = indexOf.call( seed, matched[i] );
+							seed[ idx ] = !( matches[ idx ] = matched[i] );
+						}
+					}) :
+					function( elem ) {
+						return fn( elem, 0, args );
+					};
+			}
+
+			return fn;
+		}
+	},
+
+	pseudos: {
+		// Potentially complex pseudos
+		"not": markFunction(function( selector ) {
+			// Trim the selector passed to compile
+			// to avoid treating leading and trailing
+			// spaces as combinators
+			var input = [],
+				results = [],
+				matcher = compile( selector.replace( rtrim, "$1" ) );
+
+			return matcher[ expando ] ?
+				markFunction(function( seed, matches, context, xml ) {
+					var elem,
+						unmatched = matcher( seed, null, xml, [] ),
+						i = seed.length;
+
+					// Match elements unmatched by `matcher`
+					while ( i-- ) {
+						if ( (elem = unmatched[i]) ) {
+							seed[i] = !(matches[i] = elem);
+						}
+					}
+				}) :
+				function( elem, context, xml ) {
+					input[0] = elem;
+					matcher( input, null, xml, results );
+					return !results.pop();
+				};
+		}),
+
+		"has": markFunction(function( selector ) {
+			return function( elem ) {
+				return Sizzle( selector, elem ).length > 0;
+			};
+		}),
+
+		"contains": markFunction(function( text ) {
+			return function( elem ) {
+				return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1;
+			};
+		}),
+
+		// "Whether an element is represented by a :lang() selector
+		// is based solely on the element's language value
+		// being equal to the identifier C,
+		// or beginning with the identifier C immediately followed by "-".
+		// The matching of C against the element's language value is performed case-insensitively.
+		// The identifier C does not have to be a valid language name."
+		// http://www.w3.org/TR/selectors/#lang-pseudo
+		"lang": markFunction( function( lang ) {
+			// lang value must be a valid identifier
+			if ( !ridentifier.test(lang || "") ) {
+				Sizzle.error( "unsupported lang: " + lang );
+			}
+			lang = lang.replace( runescape, funescape ).toLowerCase();
+			return function( elem ) {
+				var elemLang;
+				do {
+					if ( (elemLang = documentIsHTML ?
+						elem.lang :
+						elem.getAttribute("xml:lang") || elem.getAttribute("lang")) ) {
+
+						elemLang = elemLang.toLowerCase();
+						return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0;
+					}
+				} while ( (elem = elem.parentNode) && elem.nodeType === 1 );
+				return false;
+			};
+		}),
+
+		// Miscellaneous
+		"target": function( elem ) {
+			var hash = window.location && window.location.hash;
+			return hash && hash.slice( 1 ) === elem.id;
+		},
+
+		"root": function( elem ) {
+			return elem === docElem;
+		},
+
+		"focus": function( elem ) {
+			return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex);
+		},
+
+		// Boolean properties
+		"enabled": function( elem ) {
+			return elem.disabled === false;
+		},
+
+		"disabled": function( elem ) {
+			return elem.disabled === true;
+		},
+
+		"checked": function( elem ) {
+			// In CSS3, :checked should return both checked and selected elements
+			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+			var nodeName = elem.nodeName.toLowerCase();
+			return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected);
+		},
+
+		"selected": function( elem ) {
+			// Accessing this property makes selected-by-default
+			// options in Safari work properly
+			if ( elem.parentNode ) {
+				elem.parentNode.selectedIndex;
+			}
+
+			return elem.selected === true;
+		},
+
+		// Contents
+		"empty": function( elem ) {
+			// http://www.w3.org/TR/selectors/#empty-pseudo
+			// :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5),
+			//   but not by others (comment: 8; processing instruction: 7; etc.)
+			// nodeType < 6 works because attributes (2) do not appear as children
+			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
+				if ( elem.nodeType < 6 ) {
+					return false;
+				}
+			}
+			return true;
+		},
+
+		"parent": function( elem ) {
+			return !Expr.pseudos["empty"]( elem );
+		},
+
+		// Element/input types
+		"header": function( elem ) {
+			return rheader.test( elem.nodeName );
+		},
+
+		"input": function( elem ) {
+			return rinputs.test( elem.nodeName );
+		},
+
+		"button": function( elem ) {
+			var name = elem.nodeName.toLowerCase();
+			return name === "input" && elem.type === "button" || name === "button";
+		},
+
+		"text": function( elem ) {
+			var attr;
+			return elem.nodeName.toLowerCase() === "input" &&
+				elem.type === "text" &&
+
+				// Support: IE<8
+				// New HTML5 attribute values (e.g., "search") appear with elem.type === "text"
+				( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text" );
+		},
+
+		// Position-in-collection
+		"first": createPositionalPseudo(function() {
+			return [ 0 ];
+		}),
+
+		"last": createPositionalPseudo(function( matchIndexes, length ) {
+			return [ length - 1 ];
+		}),
+
+		"eq": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			return [ argument < 0 ? argument + length : argument ];
+		}),
+
+		"even": createPositionalPseudo(function( matchIndexes, length ) {
+			var i = 0;
+			for ( ; i < length; i += 2 ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		}),
+
+		"odd": createPositionalPseudo(function( matchIndexes, length ) {
+			var i = 1;
+			for ( ; i < length; i += 2 ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		}),
+
+		"lt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			var i = argument < 0 ? argument + length : argument;
+			for ( ; --i >= 0; ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		}),
+
+		"gt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			var i = argument < 0 ? argument + length : argument;
+			for ( ; ++i < length; ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		})
+	}
+};
+
+Expr.pseudos["nth"] = Expr.pseudos["eq"];
+
+// Add button/input type pseudos
+for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) {
+	Expr.pseudos[ i ] = createInputPseudo( i );
+}
+for ( i in { submit: true, reset: true } ) {
+	Expr.pseudos[ i ] = createButtonPseudo( i );
+}
+
+// Easy API for creating new setFilters
+function setFilters() {}
+setFilters.prototype = Expr.filters = Expr.pseudos;
+Expr.setFilters = new setFilters();
+
+tokenize = Sizzle.tokenize = function( selector, parseOnly ) {
+	var matched, match, tokens, type,
+		soFar, groups, preFilters,
+		cached = tokenCache[ selector + " " ];
+
+	if ( cached ) {
+		return parseOnly ? 0 : cached.slice( 0 );
+	}
+
+	soFar = selector;
+	groups = [];
+	preFilters = Expr.preFilter;
+
+	while ( soFar ) {
+
+		// Comma and first run
+		if ( !matched || (match = rcomma.exec( soFar )) ) {
+			if ( match ) {
+				// Don't consume trailing commas as valid
+				soFar = soFar.slice( match[0].length ) || soFar;
+			}
+			groups.push( (tokens = []) );
+		}
+
+		matched = false;
+
+		// Combinators
+		if ( (match = rcombinators.exec( soFar )) ) {
+			matched = match.shift();
+			tokens.push({
+				value: matched,
+				// Cast descendant combinators to space
+				type: match[0].replace( rtrim, " " )
+			});
+			soFar = soFar.slice( matched.length );
+		}
+
+		// Filters
+		for ( type in Expr.filter ) {
+			if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] ||
+				(match = preFilters[ type ]( match ))) ) {
+				matched = match.shift();
+				tokens.push({
+					value: matched,
+					type: type,
+					matches: match
+				});
+				soFar = soFar.slice( matched.length );
+			}
+		}
+
+		if ( !matched ) {
+			break;
+		}
+	}
+
+	// Return the length of the invalid excess
+	// if we're just parsing
+	// Otherwise, throw an error or return tokens
+	return parseOnly ?
+		soFar.length :
+		soFar ?
+			Sizzle.error( selector ) :
+			// Cache the tokens
+			tokenCache( selector, groups ).slice( 0 );
+};
+
+function toSelector( tokens ) {
+	var i = 0,
+		len = tokens.length,
+		selector = "";
+	for ( ; i < len; i++ ) {
+		selector += tokens[i].value;
+	}
+	return selector;
+}
+
+function addCombinator( matcher, combinator, base ) {
+	var dir = combinator.dir,
+		checkNonElements = base && dir === "parentNode",
+		doneName = done++;
+
+	return combinator.first ?
+		// Check against closest ancestor/preceding element
+		function( elem, context, xml ) {
+			while ( (elem = elem[ dir ]) ) {
+				if ( elem.nodeType === 1 || checkNonElements ) {
+					return matcher( elem, context, xml );
+				}
+			}
+		} :
+
+		// Check against all ancestor/preceding elements
+		function( elem, context, xml ) {
+			var oldCache, outerCache,
+				newCache = [ dirruns, doneName ];
+
+			// We can't set arbitrary data on XML nodes, so they don't benefit from dir caching
+			if ( xml ) {
+				while ( (elem = elem[ dir ]) ) {
+					if ( elem.nodeType === 1 || checkNonElements ) {
+						if ( matcher( elem, context, xml ) ) {
+							return true;
+						}
+					}
+				}
+			} else {
+				while ( (elem = elem[ dir ]) ) {
+					if ( elem.nodeType === 1 || checkNonElements ) {
+						outerCache = elem[ expando ] || (elem[ expando ] = {});
+						if ( (oldCache = outerCache[ dir ]) &&
+							oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) {
+
+							// Assign to newCache so results back-propagate to previous elements
+							return (newCache[ 2 ] = oldCache[ 2 ]);
+						} else {
+							// Reuse newcache so results back-propagate to previous elements
+							outerCache[ dir ] = newCache;
+
+							// A match means we're done; a fail means we have to keep checking
+							if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) {
+								return true;
+							}
+						}
+					}
+				}
+			}
+		};
+}
+
+function elementMatcher( matchers ) {
+	return matchers.length > 1 ?
+		function( elem, context, xml ) {
+			var i = matchers.length;
+			while ( i-- ) {
+				if ( !matchers[i]( elem, context, xml ) ) {
+					return false;
+				}
+			}
+			return true;
+		} :
+		matchers[0];
+}
+
+function multipleContexts( selector, contexts, results ) {
+	var i = 0,
+		len = contexts.length;
+	for ( ; i < len; i++ ) {
+		Sizzle( selector, contexts[i], results );
+	}
+	return results;
+}
+
+function condense( unmatched, map, filter, context, xml ) {
+	var elem,
+		newUnmatched = [],
+		i = 0,
+		len = unmatched.length,
+		mapped = map != null;
+
+	for ( ; i < len; i++ ) {
+		if ( (elem = unmatched[i]) ) {
+			if ( !filter || filter( elem, context, xml ) ) {
+				newUnmatched.push( elem );
+				if ( mapped ) {
+					map.push( i );
+				}
+			}
+		}
+	}
+
+	return newUnmatched;
+}
+
+function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {
+	if ( postFilter && !postFilter[ expando ] ) {
+		postFilter = setMatcher( postFilter );
+	}
+	if ( postFinder && !postFinder[ expando ] ) {
+		postFinder = setMatcher( postFinder, postSelector );
+	}
+	return markFunction(function( seed, results, context, xml ) {
+		var temp, i, elem,
+			preMap = [],
+			postMap = [],
+			preexisting = results.length,
+
+			// Get initial elements from seed or context
+			elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ),
+
+			// Prefilter to get matcher input, preserving a map for seed-results synchronization
+			matcherIn = preFilter && ( seed || !selector ) ?
+				condense( elems, preMap, preFilter, context, xml ) :
+				elems,
+
+			matcherOut = matcher ?
+				// If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results,
+				postFinder || ( seed ? preFilter : preexisting || postFilter ) ?
+
+					// ...intermediate processing is necessary
+					[] :
+
+					// ...otherwise use results directly
+					results :
+				matcherIn;
+
+		// Find primary matches
+		if ( matcher ) {
+			matcher( matcherIn, matcherOut, context, xml );
+		}
+
+		// Apply postFilter
+		if ( postFilter ) {
+			temp = condense( matcherOut, postMap );
+			postFilter( temp, [], context, xml );
+
+			// Un-match failing elements by moving them back to matcherIn
+			i = temp.length;
+			while ( i-- ) {
+				if ( (elem = temp[i]) ) {
+					matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem);
+				}
+			}
+		}
+
+		if ( seed ) {
+			if ( postFinder || preFilter ) {
+				if ( postFinder ) {
+					// Get the final matcherOut by condensing this intermediate into postFinder contexts
+					temp = [];
+					i = matcherOut.length;
+					while ( i-- ) {
+						if ( (elem = matcherOut[i]) ) {
+							// Restore matcherIn since elem is not yet a final match
+							temp.push( (matcherIn[i] = elem) );
+						}
+					}
+					postFinder( null, (matcherOut = []), temp, xml );
+				}
+
+				// Move matched elements from seed to results to keep them synchronized
+				i = matcherOut.length;
+				while ( i-- ) {
+					if ( (elem = matcherOut[i]) &&
+						(temp = postFinder ? indexOf.call( seed, elem ) : preMap[i]) > -1 ) {
+
+						seed[temp] = !(results[temp] = elem);
+					}
+				}
+			}
+
+		// Add elements to results, through postFinder if defined
+		} else {
+			matcherOut = condense(
+				matcherOut === results ?
+					matcherOut.splice( preexisting, matcherOut.length ) :
+					matcherOut
+			);
+			if ( postFinder ) {
+				postFinder( null, results, matcherOut, xml );
+			} else {
+				push.apply( results, matcherOut );
+			}
+		}
+	});
+}
+
+function matcherFromTokens( tokens ) {
+	var checkContext, matcher, j,
+		len = tokens.length,
+		leadingRelative = Expr.relative[ tokens[0].type ],
+		implicitRelative = leadingRelative || Expr.relative[" "],
+		i = leadingRelative ? 1 : 0,
+
+		// The foundational matcher ensures that elements are reachable from top-level context(s)
+		matchContext = addCombinator( function( elem ) {
+			return elem === checkContext;
+		}, implicitRelative, true ),
+		matchAnyContext = addCombinator( function( elem ) {
+			return indexOf.call( checkContext, elem ) > -1;
+		}, implicitRelative, true ),
+		matchers = [ function( elem, context, xml ) {
+			return ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
+				(checkContext = context).nodeType ?
+					matchContext( elem, context, xml ) :
+					matchAnyContext( elem, context, xml ) );
+		} ];
+
+	for ( ; i < len; i++ ) {
+		if ( (matcher = Expr.relative[ tokens[i].type ]) ) {
+			matchers = [ addCombinator(elementMatcher( matchers ), matcher) ];
+		} else {
+			matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches );
+
+			// Return special upon seeing a positional matcher
+			if ( matcher[ expando ] ) {
+				// Find the next relative operator (if any) for proper handling
+				j = ++i;
+				for ( ; j < len; j++ ) {
+					if ( Expr.relative[ tokens[j].type ] ) {
+						break;
+					}
+				}
+				return setMatcher(
+					i > 1 && elementMatcher( matchers ),
+					i > 1 && toSelector(
+						// If the preceding token was a descendant combinator, insert an implicit any-element `*`
+						tokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === " " ? "*" : "" })
+					).replace( rtrim, "$1" ),
+					matcher,
+					i < j && matcherFromTokens( tokens.slice( i, j ) ),
+					j < len && matcherFromTokens( (tokens = tokens.slice( j )) ),
+					j < len && toSelector( tokens )
+				);
+			}
+			matchers.push( matcher );
+		}
+	}
+
+	return elementMatcher( matchers );
+}
+
+function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
+	var bySet = setMatchers.length > 0,
+		byElement = elementMatchers.length > 0,
+		superMatcher = function( seed, context, xml, results, outermost ) {
+			var elem, j, matcher,
+				matchedCount = 0,
+				i = "0",
+				unmatched = seed && [],
+				setMatched = [],
+				contextBackup = outermostContext,
+				// We must always have either seed elements or outermost context
+				elems = seed || byElement && Expr.find["TAG"]( "*", outermost ),
+				// Use integer dirruns iff this is the outermost matcher
+				dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1),
+				len = elems.length;
+
+			if ( outermost ) {
+				outermostContext = context !== document && context;
+			}
+
+			// Add elements passing elementMatchers directly to results
+			// Keep `i` a string if there are no elements so `matchedCount` will be "00" below
+			// Support: IE<9, Safari
+			// Tolerate NodeList properties (IE: "length"; Safari: <number>) matching elements by id
+			for ( ; i !== len && (elem = elems[i]) != null; i++ ) {
+				if ( byElement && elem ) {
+					j = 0;
+					while ( (matcher = elementMatchers[j++]) ) {
+						if ( matcher( elem, context, xml ) ) {
+							results.push( elem );
+							break;
+						}
+					}
+					if ( outermost ) {
+						dirruns = dirrunsUnique;
+					}
+				}
+
+				// Track unmatched elements for set filters
+				if ( bySet ) {
+					// They will have gone through all possible matchers
+					if ( (elem = !matcher && elem) ) {
+						matchedCount--;
+					}
+
+					// Lengthen the array for every element, matched or not
+					if ( seed ) {
+						unmatched.push( elem );
+					}
+				}
+			}
+
+			// Apply set filters to unmatched elements
+			matchedCount += i;
+			if ( bySet && i !== matchedCount ) {
+				j = 0;
+				while ( (matcher = setMatchers[j++]) ) {
+					matcher( unmatched, setMatched, context, xml );
+				}
+
+				if ( seed ) {
+					// Reintegrate element matches to eliminate the need for sorting
+					if ( matchedCount > 0 ) {
+						while ( i-- ) {
+							if ( !(unmatched[i] || setMatched[i]) ) {
+								setMatched[i] = pop.call( results );
+							}
+						}
+					}
+
+					// Discard index placeholder values to get only actual matches
+					setMatched = condense( setMatched );
+				}
+
+				// Add matches to results
+				push.apply( results, setMatched );
+
+				// Seedless set matches succeeding multiple successful matchers stipulate sorting
+				if ( outermost && !seed && setMatched.length > 0 &&
+					( matchedCount + setMatchers.length ) > 1 ) {
+
+					Sizzle.uniqueSort( results );
+				}
+			}
+
+			// Override manipulation of globals by nested matchers
+			if ( outermost ) {
+				dirruns = dirrunsUnique;
+				outermostContext = contextBackup;
+			}
+
+			return unmatched;
+		};
+
+	return bySet ?
+		markFunction( superMatcher ) :
+		superMatcher;
+}
+
+compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) {
+	var i,
+		setMatchers = [],
+		elementMatchers = [],
+		cached = compilerCache[ selector + " " ];
+
+	if ( !cached ) {
+		// Generate a function of recursive functions that can be used to check each element
+		if ( !match ) {
+			match = tokenize( selector );
+		}
+		i = match.length;
+		while ( i-- ) {
+			cached = matcherFromTokens( match[i] );
+			if ( cached[ expando ] ) {
+				setMatchers.push( cached );
+			} else {
+				elementMatchers.push( cached );
+			}
+		}
+
+		// Cache the compiled function
+		cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) );
+
+		// Save selector and tokenization
+		cached.selector = selector;
+	}
+	return cached;
+};
+
+/**
+ * A low-level selection function that works with Sizzle's compiled
+ *  selector functions
+ * @param {String|Function} selector A selector or a pre-compiled
+ *  selector function built with Sizzle.compile
+ * @param {Element} context
+ * @param {Array} [results]
+ * @param {Array} [seed] A set of elements to match against
+ */
+select = Sizzle.select = function( selector, context, results, seed ) {
+	var i, tokens, token, type, find,
+		compiled = typeof selector === "function" && selector,
+		match = !seed && tokenize( (selector = compiled.selector || selector) );
+
+	results = results || [];
+
+	// Try to minimize operations if there is no seed and only one group
+	if ( match.length === 1 ) {
+
+		// Take a shortcut and set the context if the root selector is an ID
+		tokens = match[0] = match[0].slice( 0 );
+		if ( tokens.length > 2 && (token = tokens[0]).type === "ID" &&
+				support.getById && context.nodeType === 9 && documentIsHTML &&
+				Expr.relative[ tokens[1].type ] ) {
+
+			context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0];
+			if ( !context ) {
+				return results;
+
+			// Precompiled matchers will still verify ancestry, so step up a level
+			} else if ( compiled ) {
+				context = context.parentNode;
+			}
+
+			selector = selector.slice( tokens.shift().value.length );
+		}
+
+		// Fetch a seed set for right-to-left matching
+		i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length;
+		while ( i-- ) {
+			token = tokens[i];
+
+			// Abort if we hit a combinator
+			if ( Expr.relative[ (type = token.type) ] ) {
+				break;
+			}
+			if ( (find = Expr.find[ type ]) ) {
+				// Search, expanding context for leading sibling combinators
+				if ( (seed = find(
+					token.matches[0].replace( runescape, funescape ),
+					rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context
+				)) ) {
+
+					// If seed is empty or no tokens remain, we can return early
+					tokens.splice( i, 1 );
+					selector = seed.length && toSelector( tokens );
+					if ( !selector ) {
+						push.apply( results, seed );
+						return results;
+					}
+
+					break;
+				}
+			}
+		}
+	}
+
+	// Compile and execute a filtering function if one is not provided
+	// Provide `match` to avoid retokenization if we modified the selector above
+	( compiled || compile( selector, match ) )(
+		seed,
+		context,
+		!documentIsHTML,
+		results,
+		rsibling.test( selector ) && testContext( context.parentNode ) || context
+	);
+	return results;
+};
+
+// One-time assignments
+
+// Sort stability
+support.sortStable = expando.split("").sort( sortOrder ).join("") === expando;
+
+// Support: Chrome<14
+// Always assume duplicates if they aren't passed to the comparison function
+support.detectDuplicates = !!hasDuplicate;
+
+// Initialize against the default document
+setDocument();
+
+// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27)
+// Detached nodes confoundingly follow *each other*
+support.sortDetached = assert(function( div1 ) {
+	// Should return 1, but returns 4 (following)
+	return div1.compareDocumentPosition( document.createElement("div") ) & 1;
+});
+
+// Support: IE<8
+// Prevent attribute/property "interpolation"
+// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
+if ( !assert(function( div ) {
+	div.innerHTML = "<a href='#'></a>";
+	return div.firstChild.getAttribute("href") === "#" ;
+}) ) {
+	addHandle( "type|href|height|width", function( elem, name, isXML ) {
+		if ( !isXML ) {
+			return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 );
+		}
+	});
+}
+
+// Support: IE<9
+// Use defaultValue in place of getAttribute("value")
+if ( !support.attributes || !assert(function( div ) {
+	div.innerHTML = "<input/>";
+	div.firstChild.setAttribute( "value", "" );
+	return div.firstChild.getAttribute( "value" ) === "";
+}) ) {
+	addHandle( "value", function( elem, name, isXML ) {
+		if ( !isXML && elem.nodeName.toLowerCase() === "input" ) {
+			return elem.defaultValue;
+		}
+	});
+}
+
+// Support: IE<9
+// Use getAttributeNode to fetch booleans when getAttribute lies
+if ( !assert(function( div ) {
+	return div.getAttribute("disabled") == null;
+}) ) {
+	addHandle( booleans, function( elem, name, isXML ) {
+		var val;
+		if ( !isXML ) {
+			return elem[ name ] === true ? name.toLowerCase() :
+					(val = elem.getAttributeNode( name )) && val.specified ?
+					val.value :
+				null;
+		}
+	});
+}
+
+return Sizzle;
+
+})( window );
+
+
+
+jQuery.find = Sizzle;
+jQuery.expr = Sizzle.selectors;
+jQuery.expr[":"] = jQuery.expr.pseudos;
+jQuery.unique = Sizzle.uniqueSort;
+jQuery.text = Sizzle.getText;
+jQuery.isXMLDoc = Sizzle.isXML;
+jQuery.contains = Sizzle.contains;
+
+
+
+var rneedsContext = jQuery.expr.match.needsContext;
+
+var rsingleTag = (/^<(\w+)\s*\/?>(?:<\/\1>|)$/);
+
+
+
+var risSimple = /^.[^:#\[\.,]*$/;
+
+// Implement the identical functionality for filter and not
+function winnow( elements, qualifier, not ) {
+	if ( jQuery.isFunction( qualifier ) ) {
+		return jQuery.grep( elements, function( elem, i ) {
+			/* jshint -W018 */
+			return !!qualifier.call( elem, i, elem ) !== not;
+		});
+
+	}
+
+	if ( qualifier.nodeType ) {
+		return jQuery.grep( elements, function( elem ) {
+			return ( elem === qualifier ) !== not;
+		});
+
+	}
+
+	if ( typeof qualifier === "string" ) {
+		if ( risSimple.test( qualifier ) ) {
+			return jQuery.filter( qualifier, elements, not );
+		}
+
+		qualifier = jQuery.filter( qualifier, elements );
+	}
+
+	return jQuery.grep( elements, function( elem ) {
+		return ( jQuery.inArray( elem, qualifier ) >= 0 ) !== not;
+	});
+}
+
+jQuery.filter = function( expr, elems, not ) {
+	var elem = elems[ 0 ];
+
+	if ( not ) {
+		expr = ":not(" + expr + ")";
+	}
+
+	return elems.length === 1 && elem.nodeType === 1 ?
+		jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [] :
+		jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) {
+			return elem.nodeType === 1;
+		}));
+};
+
+jQuery.fn.extend({
+	find: function( selector ) {
+		var i,
+			ret = [],
+			self = this,
+			len = self.length;
+
+		if ( typeof selector !== "string" ) {
+			return this.pushStack( jQuery( selector ).filter(function() {
+				for ( i = 0; i < len; i++ ) {
+					if ( jQuery.contains( self[ i ], this ) ) {
+						return true;
+					}
+				}
+			}) );
+		}
+
+		for ( i = 0; i < len; i++ ) {
+			jQuery.find( selector, self[ i ], ret );
+		}
+
+		// Needed because $( selector, context ) becomes $( context ).find( selector )
+		ret = this.pushStack( len > 1 ? jQuery.unique( ret ) : ret );
+		ret.selector = this.selector ? this.selector + " " + selector : selector;
+		return ret;
+	},
+	filter: function( selector ) {
+		return this.pushStack( winnow(this, selector || [], false) );
+	},
+	not: function( selector ) {
+		return this.pushStack( winnow(this, selector || [], true) );
+	},
+	is: function( selector ) {
+		return !!winnow(
+			this,
+
+			// If this is a positional/relative selector, check membership in the returned set
+			// so $("p:first").is("p:last") won't return true for a doc with two "p".
+			typeof selector === "string" && rneedsContext.test( selector ) ?
+				jQuery( selector ) :
+				selector || [],
+			false
+		).length;
+	}
+});
+
+
+// Initialize a jQuery object
+
+
+// A central reference to the root jQuery(document)
+var rootjQuery,
+
+	// Use the correct document accordingly with window argument (sandbox)
+	document = window.document,
+
+	// A simple way to check for HTML strings
+	// Prioritize #id over <tag> to avoid XSS via location.hash (#9521)
+	// Strict HTML recognition (#11290: must start with <)
+	rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]*))$/,
+
+	init = jQuery.fn.init = function( selector, context ) {
+		var match, elem;
+
+		// HANDLE: $(""), $(null), $(undefined), $(false)
+		if ( !selector ) {
+			return this;
+		}
+
+		// Handle HTML strings
+		if ( typeof selector === "string" ) {
+			if ( selector.charAt(0) === "<" && selector.charAt( selector.length - 1 ) === ">" && selector.length >= 3 ) {
+				// Assume that strings that start and end with <> are HTML and skip the regex check
+				match = [ null, selector, null ];
+
+			} else {
+				match = rquickExpr.exec( selector );
+			}
+
+			// Match html or make sure no context is specified for #id
+			if ( match && (match[1] || !context) ) {
+
+				// HANDLE: $(html) -> $(array)
+				if ( match[1] ) {
+					context = context instanceof jQuery ? context[0] : context;
+
+					// scripts is true for back-compat
+					// Intentionally let the error be thrown if parseHTML is not present
+					jQuery.merge( this, jQuery.parseHTML(
+						match[1],
+						context && context.nodeType ? context.ownerDocument || context : document,
+						true
+					) );
+
+					// HANDLE: $(html, props)
+					if ( rsingleTag.test( match[1] ) && jQuery.isPlainObject( context ) ) {
+						for ( match in context ) {
+							// Properties of context are called as methods if possible
+							if ( jQuery.isFunction( this[ match ] ) ) {
+								this[ match ]( context[ match ] );
+
+							// ...and otherwise set as attributes
+							} else {
+								this.attr( match, context[ match ] );
+							}
+						}
+					}
+
+					return this;
+
+				// HANDLE: $(#id)
+				} else {
+					elem = document.getElementById( match[2] );
+
+					// Check parentNode to catch when Blackberry 4.6 returns
+					// nodes that are no longer in the document #6963
+					if ( elem && elem.parentNode ) {
+						// Handle the case where IE and Opera return items
+						// by name instead of ID
+						if ( elem.id !== match[2] ) {
+							return rootjQuery.find( selector );
+						}
+
+						// Otherwise, we inject the element directly into the jQuery object
+						this.length = 1;
+						this[0] = elem;
+					}
+
+					this.context = document;
+					this.selector = selector;
+					return this;
+				}
+
+			// HANDLE: $(expr, $(...))
+			} else if ( !context || context.jquery ) {
+				return ( context || rootjQuery ).find( selector );
+
+			// HANDLE: $(expr, context)
+			// (which is just equivalent to: $(context).find(expr)
+			} else {
+				return this.constructor( context ).find( selector );
+			}
+
+		// HANDLE: $(DOMElement)
+		} else if ( selector.nodeType ) {
+			this.context = this[0] = selector;
+			this.length = 1;
+			return this;
+
+		// HANDLE: $(function)
+		// Shortcut for document ready
+		} else if ( jQuery.isFunction( selector ) ) {
+			return typeof rootjQuery.ready !== "undefined" ?
+				rootjQuery.ready( selector ) :
+				// Execute immediately if ready is not present
+				selector( jQuery );
+		}
+
+		if ( selector.selector !== undefined ) {
+			this.selector = selector.selector;
+			this.context = selector.context;
+		}
+
+		return jQuery.makeArray( selector, this );
+	};
+
+// Give the init function the jQuery prototype for later instantiation
+init.prototype = jQuery.fn;
+
+// Initialize central reference
+rootjQuery = jQuery( document );
+
+
+var rparentsprev = /^(?:parents|prev(?:Until|All))/,
+	// methods guaranteed to produce a unique set when starting from a unique set
+	guaranteedUnique = {
+		children: true,
+		contents: true,
+		next: true,
+		prev: true
+	};
+
+jQuery.extend({
+	dir: function( elem, dir, until ) {
+		var matched = [],
+			cur = elem[ dir ];
+
+		while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) {
+			if ( cur.nodeType === 1 ) {
+				matched.push( cur );
+			}
+			cur = cur[dir];
+		}
+		return matched;
+	},
+
+	sibling: function( n, elem ) {
+		var r = [];
+
+		for ( ; n; n = n.nextSibling ) {
+			if ( n.nodeType === 1 && n !== elem ) {
+				r.push( n );
+			}
+		}
+
+		return r;
+	}
+});
+
+jQuery.fn.extend({
+	has: function( target ) {
+		var i,
+			targets = jQuery( target, this ),
+			len = targets.length;
+
+		return this.filter(function() {
+			for ( i = 0; i < len; i++ ) {
+				if ( jQuery.contains( this, targets[i] ) ) {
+					return true;
+				}
+			}
+		});
+	},
+
+	closest: function( selectors, context ) {
+		var cur,
+			i = 0,
+			l = this.length,
+			matched = [],
+			pos = rneedsContext.test( selectors ) || typeof selectors !== "string" ?
+				jQuery( selectors, context || this.context ) :
+				0;
+
+		for ( ; i < l; i++ ) {
+			for ( cur = this[i]; cur && cur !== context; cur = cur.parentNode ) {
+				// Always skip document fragments
+				if ( cur.nodeType < 11 && (pos ?
+					pos.index(cur) > -1 :
+
+					// Don't pass non-elements to Sizzle
+					cur.nodeType === 1 &&
+						jQuery.find.matchesSelector(cur, selectors)) ) {
+
+					matched.push( cur );
+					break;
+				}
+			}
+		}
+
+		return this.pushStack( matched.length > 1 ? jQuery.unique( matched ) : matched );
+	},
+
+	// Determine the position of an element within
+	// the matched set of elements
+	index: function( elem ) {
+
+		// No argument, return index in parent
+		if ( !elem ) {
+			return ( this[0] && this[0].parentNode ) ? this.first().prevAll().length : -1;
+		}
+
+		// index in selector
+		if ( typeof elem === "string" ) {
+			return jQuery.inArray( this[0], jQuery( elem ) );
+		}
+
+		// Locate the position of the desired element
+		return jQuery.inArray(
+			// If it receives a jQuery object, the first element is used
+			elem.jquery ? elem[0] : elem, this );
+	},
+
+	add: function( selector, context ) {
+		return this.pushStack(
+			jQuery.unique(
+				jQuery.merge( this.get(), jQuery( selector, context ) )
+			)
+		);
+	},
+
+	addBack: function( selector ) {
+		return this.add( selector == null ?
+			this.prevObject : this.prevObject.filter(selector)
+		);
+	}
+});
+
+function sibling( cur, dir ) {
+	do {
+		cur = cur[ dir ];
+	} while ( cur && cur.nodeType !== 1 );
+
+	return cur;
+}
+
+jQuery.each({
+	parent: function( elem ) {
+		var parent = elem.parentNode;
+		return parent && parent.nodeType !== 11 ? parent : null;
+	},
+	parents: function( elem ) {
+		return jQuery.dir( elem, "parentNode" );
+	},
+	parentsUntil: function( elem, i, until ) {
+		return jQuery.dir( elem, "parentNode", until );
+	},
+	next: function( elem ) {
+		return sibling( elem, "nextSibling" );
+	},
+	prev: function( elem ) {
+		return sibling( elem, "previousSibling" );
+	},
+	nextAll: function( elem ) {
+		return jQuery.dir( elem, "nextSibling" );
+	},
+	prevAll: function( elem ) {
+		return jQuery.dir( elem, "previousSibling" );
+	},
+	nextUntil: function( elem, i, until ) {
+		return jQuery.dir( elem, "nextSibling", until );
+	},
+	prevUntil: function( elem, i, until ) {
+		return jQuery.dir( elem, "previousSibling", until );
+	},
+	siblings: function( elem ) {
+		return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem );
+	},
+	children: function( elem ) {
+		return jQuery.sibling( elem.firstChild );
+	},
+	contents: function( elem ) {
+		return jQuery.nodeName( elem, "iframe" ) ?
+			elem.contentDocument || elem.contentWindow.document :
+			jQuery.merge( [], elem.childNodes );
+	}
+}, function( name, fn ) {
+	jQuery.fn[ name ] = function( until, selector ) {
+		var ret = jQuery.map( this, fn, until );
+
+		if ( name.slice( -5 ) !== "Until" ) {
+			selector = until;
+		}
+
+		if ( selector && typeof selector === "string" ) {
+			ret = jQuery.filter( selector, ret );
+		}
+
+		if ( this.length > 1 ) {
+			// Remove duplicates
+			if ( !guaranteedUnique[ name ] ) {
+				ret = jQuery.unique( ret );
+			}
+
+			// Reverse order for parents* and prev-derivatives
+			if ( rparentsprev.test( name ) ) {
+				ret = ret.reverse();
+			}
+		}
+
+		return this.pushStack( ret );
+	};
+});
+var rnotwhite = (/\S+/g);
+
+
+
+// String to Object options format cache
+var optionsCache = {};
+
+// Convert String-formatted options into Object-formatted ones and store in cache
+function createOptions( options ) {
+	var object = optionsCache[ options ] = {};
+	jQuery.each( options.match( rnotwhite ) || [], function( _, flag ) {
+		object[ flag ] = true;
+	});
+	return object;
+}
+
+/*
+ * Create a callback list using the following parameters:
+ *
+ *	options: an optional list of space-separated options that will change how
+ *			the callback list behaves or a more traditional option object
+ *
+ * By default a callback list will act like an event callback list and can be
+ * "fired" multiple times.
+ *
+ * Possible options:
+ *
+ *	once:			will ensure the callback list can only be fired once (like a Deferred)
+ *
+ *	memory:			will keep track of previous values and will call any callback added
+ *					after the list has been fired right away with the latest "memorized"
+ *					values (like a Deferred)
+ *
+ *	unique:			will ensure a callback can only be added once (no duplicate in the list)
+ *
+ *	stopOnFalse:	interrupt callings when a callback returns false
+ *
+ */
+jQuery.Callbacks = function( options ) {
+
+	// Convert options from String-formatted to Object-formatted if needed
+	// (we check in cache first)
+	options = typeof options === "string" ?
+		( optionsCache[ options ] || createOptions( options ) ) :
+		jQuery.extend( {}, options );
+
+	var // Flag to know if list is currently firing
+		firing,
+		// Last fire value (for non-forgettable lists)
+		memory,
+		// Flag to know if list was already fired
+		fired,
+		// End of the loop when firing
+		firingLength,
+		// Index of currently firing callback (modified by remove if needed)
+		firingIndex,
+		// First callback to fire (used internally by add and fireWith)
+		firingStart,
+		// Actual callback list
+		list = [],
+		// Stack of fire calls for repeatable lists
+		stack = !options.once && [],
+		// Fire callbacks
+		fire = function( data ) {
+			memory = options.memory && data;
+			fired = true;
+			firingIndex = firingStart || 0;
+			firingStart = 0;
+			firingLength = list.length;
+			firing = true;
+			for ( ; list && firingIndex < firingLength; firingIndex++ ) {
+				if ( list[ firingIndex ].apply( data[ 0 ], data[ 1 ] ) === false && options.stopOnFalse ) {
+					memory = false; // To prevent further calls using add
+					break;
+				}
+			}
+			firing = false;
+			if ( list ) {
+				if ( stack ) {
+					if ( stack.length ) {
+						fire( stack.shift() );
+					}
+				} else if ( memory ) {
+					list = [];
+				} else {
+					self.disable();
+				}
+			}
+		},
+		// Actual Callbacks object
+		self = {
+			// Add a callback or a collection of callbacks to the list
+			add: function() {
+				if ( list ) {
+					// First, we save the current length
+					var start = list.length;
+					(function add( args ) {
+						jQuery.each( args, function( _, arg ) {
+							var type = jQuery.type( arg );
+							if ( type === "function" ) {
+								if ( !options.unique || !self.has( arg ) ) {
+									list.push( arg );
+								}
+							} else if ( arg && arg.length && type !== "string" ) {
+								// Inspect recursively
+								add( arg );
+							}
+						});
+					})( arguments );
+					// Do we need to add the callbacks to the
+					// current firing batch?
+					if ( firing ) {
+						firingLength = list.length;
+					// With memory, if we're not firing then
+					// we should call right away
+					} else if ( memory ) {
+						firingStart = start;
+						fire( memory );
+					}
+				}
+				return this;
+			},
+			// Remove a callback from the list
+			remove: function() {
+				if ( list ) {
+					jQuery.each( arguments, function( _, arg ) {
+						var index;
+						while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
+							list.splice( index, 1 );
+							// Handle firing indexes
+							if ( firing ) {
+								if ( index <= firingLength ) {
+									firingLength--;
+								}
+								if ( index <= firingIndex ) {
+									firingIndex--;
+								}
+							}
+						}
+					});
+				}
+				return this;
+			},
+			// Check if a given callback is in the list.
+			// If no argument is given, return whether or not list has callbacks attached.
+			has: function( fn ) {
+				return fn ? jQuery.inArray( fn, list ) > -1 : !!( list && list.length );
+			},
+			// Remove all callbacks from the list
+			empty: function() {
+				list = [];
+				firingLength = 0;
+				return this;
+			},
+			// Have the list do nothing anymore
+			disable: function() {
+				list = stack = memory = undefined;
+				return this;
+			},
+			// Is it disabled?
+			disabled: function() {
+				return !list;
+			},
+			// Lock the list in its current state
+			lock: function() {
+				stack = undefined;
+				if ( !memory ) {
+					self.disable();
+				}
+				return this;
+			},
+			// Is it locked?
+			locked: function() {
+				return !stack;
+			},
+			// Call all callbacks with the given context and arguments
+			fireWith: function( context, args ) {
+				if ( list && ( !fired || stack ) ) {
+					args = args || [];
+					args = [ context, args.slice ? args.slice() : args ];
+					if ( firing ) {
+						stack.push( args );
+					} else {
+						fire( args );
+					}
+				}
+				return this;
+			},
+			// Call all the callbacks with the given arguments
+			fire: function() {
+				self.fireWith( this, arguments );
+				return this;
+			},
+			// To know if the callbacks have already been called at least once
+			fired: function() {
+				return !!fired;
+			}
+		};
+
+	return self;
+};
+
+
+jQuery.extend({
+
+	Deferred: function( func ) {
+		var tuples = [
+				// action, add listener, listener list, final state
+				[ "resolve", "done", jQuery.Callbacks("once memory"), "resolved" ],
+				[ "reject", "fail", jQuery.Callbacks("once memory"), "rejected" ],
+				[ "notify", "progress", jQuery.Callbacks("memory") ]
+			],
+			state = "pending",
+			promise = {
+				state: function() {
+					return state;
+				},
+				always: function() {
+					deferred.done( arguments ).fail( arguments );
+					return this;
+				},
+				then: function( /* fnDone, fnFail, fnProgress */ ) {
+					var fns = arguments;
+					return jQuery.Deferred(function( newDefer ) {
+						jQuery.each( tuples, function( i, tuple ) {
+							var fn = jQuery.isFunction( fns[ i ] ) && fns[ i ];
+							// deferred[ done | fail | progress ] for forwarding actions to newDefer
+							deferred[ tuple[1] ](function() {
+								var returned = fn && fn.apply( this, arguments );
+								if ( returned && jQuery.isFunction( returned.promise ) ) {
+									returned.promise()
+										.done( newDefer.resolve )
+										.fail( newDefer.reject )
+										.progress( newDefer.notify );
+								} else {
+									newDefer[ tuple[ 0 ] + "With" ]( this === promise ? newDefer.promise() : this, fn ? [ returned ] : arguments );
+								}
+							});
+						});
+						fns = null;
+					}).promise();
+				},
+				// Get a promise for this deferred
+				// If obj is provided, the promise aspect is added to the object
+				promise: function( obj ) {
+					return obj != null ? jQuery.extend( obj, promise ) : promise;
+				}
+			},
+			deferred = {};
+
+		// Keep pipe for back-compat
+		promise.pipe = promise.then;
+
+		// Add list-specific methods
+		jQuery.each( tuples, function( i, tuple ) {
+			var list = tuple[ 2 ],
+				stateString = tuple[ 3 ];
+
+			// promise[ done | fail | progress ] = list.add
+			promise[ tuple[1] ] = list.add;
+
+			// Handle state
+			if ( stateString ) {
+				list.add(function() {
+					// state = [ resolved | rejected ]
+					state = stateString;
+
+				// [ reject_list | resolve_list ].disable; progress_list.lock
+				}, tuples[ i ^ 1 ][ 2 ].disable, tuples[ 2 ][ 2 ].lock );
+			}
+
+			// deferred[ resolve | reject | notify ]
+			deferred[ tuple[0] ] = function() {
+				deferred[ tuple[0] + "With" ]( this === deferred ? promise : this, arguments );
+				return this;
+			};
+			deferred[ tuple[0] + "With" ] = list.fireWith;
+		});
+
+		// Make the deferred a promise
+		promise.promise( deferred );
+
+		// Call given func if any
+		if ( func ) {
+			func.call( deferred, deferred );
+		}
+
+		// All done!
+		return deferred;
+	},
+
+	// Deferred helper
+	when: function( subordinate /* , ..., subordinateN */ ) {
+		var i = 0,
+			resolveValues = slice.call( arguments ),
+			length = resolveValues.length,
+
+			// the count of uncompleted subordinates
+			remaining = length !== 1 || ( subordinate && jQuery.isFunction( subordinate.promise ) ) ? length : 0,
+
+			// the master Deferred. If resolveValues consist of only a single Deferred, just use that.
+			deferred = remaining === 1 ? subordinate : jQuery.Deferred(),
+
+			// Update function for both resolve and progress values
+			updateFunc = function( i, contexts, values ) {
+				return function( value ) {
+					contexts[ i ] = this;
+					values[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
+					if ( values === progressValues ) {
+						deferred.notifyWith( contexts, values );
+
+					} else if ( !(--remaining) ) {
+						deferred.resolveWith( contexts, values );
+					}
+				};
+			},
+
+			progressValues, progressContexts, resolveContexts;
+
+		// add listeners to Deferred subordinates; treat others as resolved
+		if ( length > 1 ) {
+			progressValues = new Array( length );
+			progressContexts = new Array( length );
+			resolveContexts = new Array( length );
+			for ( ; i < length; i++ ) {
+				if ( resolveValues[ i ] && jQuery.isFunction( resolveValues[ i ].promise ) ) {
+					resolveValues[ i ].promise()
+						.done( updateFunc( i, resolveContexts, resolveValues ) )
+						.fail( deferred.reject )
+						.progress( updateFunc( i, progressContexts, progressValues ) );
+				} else {
+					--remaining;
+				}
+			}
+		}
+
+		// if we're not waiting on anything, resolve the master
+		if ( !remaining ) {
+			deferred.resolveWith( resolveContexts, resolveValues );
+		}
+
+		return deferred.promise();
+	}
+});
+
+
+// The deferred used on DOM ready
+var readyList;
+
+jQuery.fn.ready = function( fn ) {
+	// Add the callback
+	jQuery.ready.promise().done( fn );
+
+	return this;
+};
+
+jQuery.extend({
+	// Is the DOM ready to be used? Set to true once it occurs.
+	isReady: false,
+
+	// A counter to track how many items to wait for before
+	// the ready event fires. See #6781
+	readyWait: 1,
+
+	// Hold (or release) the ready event
+	holdReady: function( hold ) {
+		if ( hold ) {
+			jQuery.readyWait++;
+		} else {
+			jQuery.ready( true );
+		}
+	},
+
+	// Handle when the DOM is ready
+	ready: function( wait ) {
+
+		// Abort if there are pending holds or we're already ready
+		if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {
+			return;
+		}
+
+		// Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443).
+		if ( !document.body ) {
+			return setTimeout( jQuery.ready );
+		}
+
+		// Remember that the DOM is ready
+		jQuery.isReady = true;
+
+		// If a normal DOM Ready event fired, decrement, and wait if need be
+		if ( wait !== true && --jQuery.readyWait > 0 ) {
+			return;
+		}
+
+		// If there are functions bound, to execute
+		readyList.resolveWith( document, [ jQuery ] );
+
+		// Trigger any bound ready events
+		if ( jQuery.fn.triggerHandler ) {
+			jQuery( document ).triggerHandler( "ready" );
+			jQuery( document ).off( "ready" );
+		}
+	}
+});
+
+/**
+ * Clean-up method for dom ready events
+ */
+function detach() {
+	if ( document.addEventListener ) {
+		document.removeEventListener( "DOMContentLoaded", completed, false );
+		window.removeEventListener( "load", completed, false );
+
+	} else {
+		document.detachEvent( "onreadystatechange", completed );
+		window.detachEvent( "onload", completed );
+	}
+}
+
+/**
+ * The ready event handler and self cleanup method
+ */
+function completed() {
+	// readyState === "complete" is good enough for us to call the dom ready in oldIE
+	if ( document.addEventListener || event.type === "load" || document.readyState === "complete" ) {
+		detach();
+		jQuery.ready();
+	}
+}
+
+jQuery.ready.promise = function( obj ) {
+	if ( !readyList ) {
+
+		readyList = jQuery.Deferred();
+
+		// Catch cases where $(document).ready() is called after the browser event has already occurred.
+		// we once tried to use readyState "interactive" here, but it caused issues like the one
+		// discovered by ChrisS here: http://bugs.jquery.com/ticket/12282#comment:15
+		if ( document.readyState === "complete" ) {
+			// Handle it asynchronously to allow scripts the opportunity to delay ready
+			setTimeout( jQuery.ready );
+
+		// Standards-based browsers support DOMContentLoaded
+		} else if ( document.addEventListener ) {
+			// Use the handy event callback
+			document.addEventListener( "DOMContentLoaded", completed, false );
+
+			// A fallback to window.onload, that will always work
+			window.addEventListener( "load", completed, false );
+
+		// If IE event model is used
+		} else {
+			// Ensure firing before onload, maybe late but safe also for iframes
+			document.attachEvent( "onreadystatechange", completed );
+
+			// A fallback to window.onload, that will always work
+			window.attachEvent( "onload", completed );
+
+			// If IE and not a frame
+			// continually check to see if the document is ready
+			var top = false;
+
+			try {
+				top = window.frameElement == null && document.documentElement;
+			} catch(e) {}
+
+			if ( top && top.doScroll ) {
+				(function doScrollCheck() {
+					if ( !jQuery.isReady ) {
+
+						try {
+							// Use the trick by Diego Perini
+							// http://javascript.nwbox.com/IEContentLoaded/
+							top.doScroll("left");
+						} catch(e) {
+							return setTimeout( doScrollCheck, 50 );
+						}
+
+						// detach all dom ready events
+						detach();
+
+						// and execute any waiting functions
+						jQuery.ready();
+					}
+				})();
+			}
+		}
+	}
+	return readyList.promise( obj );
+};
+
+
+var strundefined = typeof undefined;
+
+
+
+// Support: IE<9
+// Iteration over object's inherited properties before its own
+var i;
+for ( i in jQuery( support ) ) {
+	break;
+}
+support.ownLast = i !== "0";
+
+// Note: most support tests are defined in their respective modules.
+// false until the test is run
+support.inlineBlockNeedsLayout = false;
+
+// Execute ASAP in case we need to set body.style.zoom
+jQuery(function() {
+	// Minified: var a,b,c,d
+	var val, div, body, container;
+
+	body = document.getElementsByTagName( "body" )[ 0 ];
+	if ( !body || !body.style ) {
+		// Return for frameset docs that don't have a body
+		return;
+	}
+
+	// Setup
+	div = document.createElement( "div" );
+	container = document.createElement( "div" );
+	container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
+	body.appendChild( container ).appendChild( div );
+
+	if ( typeof div.style.zoom !== strundefined ) {
+		// Support: IE<8
+		// Check if natively block-level elements act like inline-block
+		// elements when setting their display to 'inline' and giving
+		// them layout
+		div.style.cssText = "display:inline;margin:0;border:0;padding:1px;width:1px;zoom:1";
+
+		support.inlineBlockNeedsLayout = val = div.offsetWidth === 3;
+		if ( val ) {
+			// Prevent IE 6 from affecting layout for positioned elements #11048
+			// Prevent IE from shrinking the body in IE 7 mode #12869
+			// Support: IE<8
+			body.style.zoom = 1;
+		}
+	}
+
+	body.removeChild( container );
+});
+
+
+
+
+(function() {
+	var div = document.createElement( "div" );
+
+	// Execute the test only if not already executed in another module.
+	if (support.deleteExpando == null) {
+		// Support: IE<9
+		support.deleteExpando = true;
+		try {
+			delete div.test;
+		} catch( e ) {
+			support.deleteExpando = false;
+		}
+	}
+
+	// Null elements to avoid leaks in IE.
+	div = null;
+})();
+
+
+/**
+ * Determines whether an object can have data
+ */
+jQuery.acceptData = function( elem ) {
+	var noData = jQuery.noData[ (elem.nodeName + " ").toLowerCase() ],
+		nodeType = +elem.nodeType || 1;
+
+	// Do not set data on non-element DOM nodes because it will not be cleared (#8335).
+	return nodeType !== 1 && nodeType !== 9 ?
+		false :
+
+		// Nodes accept data unless otherwise specified; rejection can be conditional
+		!noData || noData !== true && elem.getAttribute("classid") === noData;
+};
+
+
+var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,
+	rmultiDash = /([A-Z])/g;
+
+function dataAttr( elem, key, data ) {
+	// If nothing was found internally, try to fetch any
+	// data from the HTML5 data-* attribute
+	if ( data === undefined && elem.nodeType === 1 ) {
+
+		var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase();
+
+		data = elem.getAttribute( name );
+
+		if ( typeof data === "string" ) {
+			try {
+				data = data === "true" ? true :
+					data === "false" ? false :
+					data === "null" ? null :
+					// Only convert to a number if it doesn't change the string
+					+data + "" === data ? +data :
+					rbrace.test( data ) ? jQuery.parseJSON( data ) :
+					data;
+			} catch( e ) {}
+
+			// Make sure we set the data so it isn't changed later
+			jQuery.data( elem, key, data );
+
+		} else {
+			data = undefined;
+		}
+	}
+
+	return data;
+}
+
+// checks a cache object for emptiness
+function isEmptyDataObject( obj ) {
+	var name;
+	for ( name in obj ) {
+
+		// if the public data object is empty, the private is still empty
+		if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) {
+			continue;
+		}
+		if ( name !== "toJSON" ) {
+			return false;
+		}
+	}
+
+	return true;
+}
+
+function internalData( elem, name, data, pvt /* Internal Use Only */ ) {
+	if ( !jQuery.acceptData( elem ) ) {
+		return;
+	}
+
+	var ret, thisCache,
+		internalKey = jQuery.expando,
+
+		// We have to handle DOM nodes and JS objects differently because IE6-7
+		// can't GC object references properly across the DOM-JS boundary
+		isNode = elem.nodeType,
+
+		// Only DOM nodes need the global jQuery cache; JS object data is
+		// attached directly to the object so GC can occur automatically
+		cache = isNode ? jQuery.cache : elem,
+
+		// Only defining an ID for JS objects if its cache already exists allows
+		// the code to shortcut on the same path as a DOM node with no cache
+		id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey;
+
+	// Avoid doing any more work than we need to when trying to get data on an
+	// object that has no data at all
+	if ( (!id || !cache[id] || (!pvt && !cache[id].data)) && data === undefined && typeof name === "string" ) {
+		return;
+	}
+
+	if ( !id ) {
+		// Only DOM nodes need a new unique ID for each element since their data
+		// ends up in the global cache
+		if ( isNode ) {
+			id = elem[ internalKey ] = deletedIds.pop() || jQuery.guid++;
+		} else {
+			id = internalKey;
+		}
+	}
+
+	if ( !cache[ id ] ) {
+		// Avoid exposing jQuery metadata on plain JS objects when the object
+		// is serialized using JSON.stringify
+		cache[ id ] = isNode ? {} : { toJSON: jQuery.noop };
+	}
+
+	// An object can be passed to jQuery.data instead of a key/value pair; this gets
+	// shallow copied over onto the existing cache
+	if ( typeof name === "object" || typeof name === "function" ) {
+		if ( pvt ) {
+			cache[ id ] = jQuery.extend( cache[ id ], name );
+		} else {
+			cache[ id ].data = jQuery.extend( cache[ id ].data, name );
+		}
+	}
+
+	thisCache = cache[ id ];
+
+	// jQuery data() is stored in a separate object inside the object's internal data
+	// cache in order to avoid key collisions between internal data and user-defined
+	// data.
+	if ( !pvt ) {
+		if ( !thisCache.data ) {
+			thisCache.data = {};
+		}
+
+		thisCache = thisCache.data;
+	}
+
+	if ( data !== undefined ) {
+		thisCache[ jQuery.camelCase( name ) ] = data;
+	}
+
+	// Check for both converted-to-camel and non-converted data property names
+	// If a data property was specified
+	if ( typeof name === "string" ) {
+
+		// First Try to find as-is property data
+		ret = thisCache[ name ];
+
+		// Test for null|undefined property data
+		if ( ret == null ) {
+
+			// Try to find the camelCased property
+			ret = thisCache[ jQuery.camelCase( name ) ];
+		}
+	} else {
+		ret = thisCache;
+	}
+
+	return ret;
+}
+
+function internalRemoveData( elem, name, pvt ) {
+	if ( !jQuery.acceptData( elem ) ) {
+		return;
+	}
+
+	var thisCache, i,
+		isNode = elem.nodeType,
+
+		// See jQuery.data for more information
+		cache = isNode ? jQuery.cache : elem,
+		id = isNode ? elem[ jQuery.expando ] : jQuery.expando;
+
+	// If there is already no cache entry for this object, there is no
+	// purpose in continuing
+	if ( !cache[ id ] ) {
+		return;
+	}
+
+	if ( name ) {
+
+		thisCache = pvt ? cache[ id ] : cache[ id ].data;
+
+		if ( thisCache ) {
+
+			// Support array or space separated string names for data keys
+			if ( !jQuery.isArray( name ) ) {
+
+				// try the string as a key before any manipulation
+				if ( name in thisCache ) {
+					name = [ name ];
+				} else {
+
+					// split the camel cased version by spaces unless a key with the spaces exists
+					name = jQuery.camelCase( name );
+					if ( name in thisCache ) {
+						name = [ name ];
+					} else {
+						name = name.split(" ");
+					}
+				}
+			} else {
+				// If "name" is an array of keys...
+				// When data is initially created, via ("key", "val") signature,
+				// keys will be converted to camelCase.
+				// Since there is no way to tell _how_ a key was added, remove
+				// both plain key and camelCase key. #12786
+				// This will only penalize the array argument path.
+				name = name.concat( jQuery.map( name, jQuery.camelCase ) );
+			}
+
+			i = name.length;
+			while ( i-- ) {
+				delete thisCache[ name[i] ];
+			}
+
+			// If there is no data left in the cache, we want to continue
+			// and let the cache object itself get destroyed
+			if ( pvt ? !isEmptyDataObject(thisCache) : !jQuery.isEmptyObject(thisCache) ) {
+				return;
+			}
+		}
+	}
+
+	// See jQuery.data for more information
+	if ( !pvt ) {
+		delete cache[ id ].data;
+
+		// Don't destroy the parent cache unless the internal data object
+		// had been the only thing left in it
+		if ( !isEmptyDataObject( cache[ id ] ) ) {
+			return;
+		}
+	}
+
+	// Destroy the cache
+	if ( isNode ) {
+		jQuery.cleanData( [ elem ], true );
+
+	// Use delete when supported for expandos or `cache` is not a window per isWindow (#10080)
+	/* jshint eqeqeq: false */
+	} else if ( support.deleteExpando || cache != cache.window ) {
+		/* jshint eqeqeq: true */
+		delete cache[ id ];
+
+	// When all else fails, null
+	} else {
+		cache[ id ] = null;
+	}
+}
+
+jQuery.extend({
+	cache: {},
+
+	// The following elements (space-suffixed to avoid Object.prototype collisions)
+	// throw uncatchable exceptions if you attempt to set expando properties
+	noData: {
+		"applet ": true,
+		"embed ": true,
+		// ...but Flash objects (which have this classid) *can* handle expandos
+		"object ": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
+	},
+
+	hasData: function( elem ) {
+		elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ];
+		return !!elem && !isEmptyDataObject( elem );
+	},
+
+	data: function( elem, name, data ) {
+		return internalData( elem, name, data );
+	},
+
+	removeData: function( elem, name ) {
+		return internalRemoveData( elem, name );
+	},
+
+	// For internal use only.
+	_data: function( elem, name, data ) {
+		return internalData( elem, name, data, true );
+	},
+
+	_removeData: function( elem, name ) {
+		return internalRemoveData( elem, name, true );
+	}
+});
+
+jQuery.fn.extend({
+	data: function( key, value ) {
+		var i, name, data,
+			elem = this[0],
+			attrs = elem && elem.attributes;
+
+		// Special expections of .data basically thwart jQuery.access,
+		// so implement the relevant behavior ourselves
+
+		// Gets all values
+		if ( key === undefined ) {
+			if ( this.length ) {
+				data = jQuery.data( elem );
+
+				if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) {
+					i = attrs.length;
+					while ( i-- ) {
+
+						// Support: IE11+
+						// The attrs elements can be null (#14894)
+						if ( attrs[ i ] ) {
+							name = attrs[ i ].name;
+							if ( name.indexOf( "data-" ) === 0 ) {
+								name = jQuery.camelCase( name.slice(5) );
+								dataAttr( elem, name, data[ name ] );
+							}
+						}
+					}
+					jQuery._data( elem, "parsedAttrs", true );
+				}
+			}
+
+			return data;
+		}
+
+		// Sets multiple values
+		if ( typeof key === "object" ) {
+			return this.each(function() {
+				jQuery.data( this, key );
+			});
+		}
+
+		return arguments.length > 1 ?
+
+			// Sets one value
+			this.each(function() {
+				jQuery.data( this, key, value );
+			}) :
+
+			// Gets one value
+			// Try to fetch any internally stored data first
+			elem ? dataAttr( elem, key, jQuery.data( elem, key ) ) : undefined;
+	},
+
+	removeData: function( key ) {
+		return this.each(function() {
+			jQuery.removeData( this, key );
+		});
+	}
+});
+
+
+jQuery.extend({
+	queue: function( elem, type, data ) {
+		var queue;
+
+		if ( elem ) {
+			type = ( type || "fx" ) + "queue";
+			queue = jQuery._data( elem, type );
+
+			// Speed up dequeue by getting out quickly if this is just a lookup
+			if ( data ) {
+				if ( !queue || jQuery.isArray(data) ) {
+					queue = jQuery._data( elem, type, jQuery.makeArray(data) );
+				} else {
+					queue.push( data );
+				}
+			}
+			return queue || [];
+		}
+	},
+
+	dequeue: function( elem, type ) {
+		type = type || "fx";
+
+		var queue = jQuery.queue( elem, type ),
+			startLength = queue.length,
+			fn = queue.shift(),
+			hooks = jQuery._queueHooks( elem, type ),
+			next = function() {
+				jQuery.dequeue( elem, type );
+			};
+
+		// If the fx queue is dequeued, always remove the progress sentinel
+		if ( fn === "inprogress" ) {
+			fn = queue.shift();
+			startLength--;
+		}
+
+		if ( fn ) {
+
+			// Add a progress sentinel to prevent the fx queue from being
+			// automatically dequeued
+			if ( type === "fx" ) {
+				queue.unshift( "inprogress" );
+			}
+
+			// clear up the last queue stop function
+			delete hooks.stop;
+			fn.call( elem, next, hooks );
+		}
+
+		if ( !startLength && hooks ) {
+			hooks.empty.fire();
+		}
+	},
+
+	// not intended for public consumption - generates a queueHooks object, or returns the current one
+	_queueHooks: function( elem, type ) {
+		var key = type + "queueHooks";
+		return jQuery._data( elem, key ) || jQuery._data( elem, key, {
+			empty: jQuery.Callbacks("once memory").add(function() {
+				jQuery._removeData( elem, type + "queue" );
+				jQuery._removeData( elem, key );
+			})
+		});
+	}
+});
+
+jQuery.fn.extend({
+	queue: function( type, data ) {
+		var setter = 2;
+
+		if ( typeof type !== "string" ) {
+			data = type;
+			type = "fx";
+			setter--;
+		}
+
+		if ( arguments.length < setter ) {
+			return jQuery.queue( this[0], type );
+		}
+
+		return data === undefined ?
+			this :
+			this.each(function() {
+				var queue = jQuery.queue( this, type, data );
+
+				// ensure a hooks for this queue
+				jQuery._queueHooks( this, type );
+
+				if ( type === "fx" && queue[0] !== "inprogress" ) {
+					jQuery.dequeue( this, type );
+				}
+			});
+	},
+	dequeue: function( type ) {
+		return this.each(function() {
+			jQuery.dequeue( this, type );
+		});
+	},
+	clearQueue: function( type ) {
+		return this.queue( type || "fx", [] );
+	},
+	// Get a promise resolved when queues of a certain type
+	// are emptied (fx is the type by default)
+	promise: function( type, obj ) {
+		var tmp,
+			count = 1,
+			defer = jQuery.Deferred(),
+			elements = this,
+			i = this.length,
+			resolve = function() {
+				if ( !( --count ) ) {
+					defer.resolveWith( elements, [ elements ] );
+				}
+			};
+
+		if ( typeof type !== "string" ) {
+			obj = type;
+			type = undefined;
+		}
+		type = type || "fx";
+
+		while ( i-- ) {
+			tmp = jQuery._data( elements[ i ], type + "queueHooks" );
+			if ( tmp && tmp.empty ) {
+				count++;
+				tmp.empty.add( resolve );
+			}
+		}
+		resolve();
+		return defer.promise( obj );
+	}
+});
+var pnum = (/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/).source;
+
+var cssExpand = [ "Top", "Right", "Bottom", "Left" ];
+
+var isHidden = function( elem, el ) {
+		// isHidden might be called from jQuery#filter function;
+		// in that case, element will be second argument
+		elem = el || elem;
+		return jQuery.css( elem, "display" ) === "none" || !jQuery.contains( elem.ownerDocument, elem );
+	};
+
+
+
+// Multifunctional method to get and set values of a collection
+// The value/s can optionally be executed if it's a function
+var access = jQuery.access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
+	var i = 0,
+		length = elems.length,
+		bulk = key == null;
+
+	// Sets many values
+	if ( jQuery.type( key ) === "object" ) {
+		chainable = true;
+		for ( i in key ) {
+			jQuery.access( elems, fn, i, key[i], true, emptyGet, raw );
+		}
+
+	// Sets one value
+	} else if ( value !== undefined ) {
+		chainable = true;
+
+		if ( !jQuery.isFunction( value ) ) {
+			raw = true;
+		}
+
+		if ( bulk ) {
+			// Bulk operations run against the entire set
+			if ( raw ) {
+				fn.call( elems, value );
+				fn = null;
+
+			// ...except when executing function values
+			} else {
+				bulk = fn;
+				fn = function( elem, key, value ) {
+					return bulk.call( jQuery( elem ), value );
+				};
+			}
+		}
+
+		if ( fn ) {
+			for ( ; i < length; i++ ) {
+				fn( elems[i], key, raw ? value : value.call( elems[i], i, fn( elems[i], key ) ) );
+			}
+		}
+	}
+
+	return chainable ?
+		elems :
+
+		// Gets
+		bulk ?
+			fn.call( elems ) :
+			length ? fn( elems[0], key ) : emptyGet;
+};
+var rcheckableType = (/^(?:checkbox|radio)$/i);
+
+
+
+(function() {
+	// Minified: var a,b,c
+	var input = document.createElement( "input" ),
+		div = document.createElement( "div" ),
+		fragment = document.createDocumentFragment();
+
+	// Setup
+	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
+
+	// IE strips leading whitespace when .innerHTML is used
+	support.leadingWhitespace = div.firstChild.nodeType === 3;
+
+	// Make sure that tbody elements aren't automatically inserted
+	// IE will insert them into empty tables
+	support.tbody = !div.getElementsByTagName( "tbody" ).length;
+
+	// Make sure that link elements get serialized correctly by innerHTML
+	// This requires a wrapper element in IE
+	support.htmlSerialize = !!div.getElementsByTagName( "link" ).length;
+
+	// Makes sure cloning an html5 element does not cause problems
+	// Where outerHTML is undefined, this still works
+	support.html5Clone =
+		document.createElement( "nav" ).cloneNode( true ).outerHTML !== "<:nav></:nav>";
+
+	// Check if a disconnected checkbox will retain its checked
+	// value of true after appended to the DOM (IE6/7)
+	input.type = "checkbox";
+	input.checked = true;
+	fragment.appendChild( input );
+	support.appendChecked = input.checked;
+
+	// Make sure textarea (and checkbox) defaultValue is properly cloned
+	// Support: IE6-IE11+
+	div.innerHTML = "<textarea>x</textarea>";
+	support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;
+
+	// #11217 - WebKit loses check when the name is after the checked attribute
+	fragment.appendChild( div );
+	div.innerHTML = "<input type='radio' checked='checked' name='t'/>";
+
+	// Support: Safari 5.1, iOS 5.1, Android 4.x, Android 2.3
+	// old WebKit doesn't clone checked state correctly in fragments
+	support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;
+
+	// Support: IE<9
+	// Opera does not clone events (and typeof div.attachEvent === undefined).
+	// IE9-10 clones events bound via attachEvent, but they don't trigger with .click()
+	support.noCloneEvent = true;
+	if ( div.attachEvent ) {
+		div.attachEvent( "onclick", function() {
+			support.noCloneEvent = false;
+		});
+
+		div.cloneNode( true ).click();
+	}
+
+	// Execute the test only if not already executed in another module.
+	if (support.deleteExpando == null) {
+		// Support: IE<9
+		support.deleteExpando = true;
+		try {
+			delete div.test;
+		} catch( e ) {
+			support.deleteExpando = false;
+		}
+	}
+})();
+
+
+(function() {
+	var i, eventName,
+		div = document.createElement( "div" );
+
+	// Support: IE<9 (lack submit/change bubble), Firefox 23+ (lack focusin event)
+	for ( i in { submit: true, change: true, focusin: true }) {
+		eventName = "on" + i;
+
+		if ( !(support[ i + "Bubbles" ] = eventName in window) ) {
+			// Beware of CSP restrictions (https://developer.mozilla.org/en/Security/CSP)
+			div.setAttribute( eventName, "t" );
+			support[ i + "Bubbles" ] = div.attributes[ eventName ].expando === false;
+		}
+	}
+
+	// Null elements to avoid leaks in IE.
+	div = null;
+})();
+
+
+var rformElems = /^(?:input|select|textarea)$/i,
+	rkeyEvent = /^key/,
+	rmouseEvent = /^(?:mouse|pointer|contextmenu)|click/,
+	rfocusMorph = /^(?:focusinfocus|focusoutblur)$/,
+	rtypenamespace = /^([^.]*)(?:\.(.+)|)$/;
+
+function returnTrue() {
+	return true;
+}
+
+function returnFalse() {
+	return false;
+}
+
+function safeActiveElement() {
+	try {
+		return document.activeElement;
+	} catch ( err ) { }
+}
+
+/*
+ * Helper functions for managing events -- not part of the public interface.
+ * Props to Dean Edwards' addEvent library for many of the ideas.
+ */
+jQuery.event = {
+
+	global: {},
+
+	add: function( elem, types, handler, data, selector ) {
+		var tmp, events, t, handleObjIn,
+			special, eventHandle, handleObj,
+			handlers, type, namespaces, origType,
+			elemData = jQuery._data( elem );
+
+		// Don't attach events to noData or text/comment nodes (but allow plain objects)
+		if ( !elemData ) {
+			return;
+		}
+
+		// Caller can pass in an object of custom data in lieu of the handler
+		if ( handler.handler ) {
+			handleObjIn = handler;
+			handler = handleObjIn.handler;
+			selector = handleObjIn.selector;
+		}
+
+		// Make sure that the handler has a unique ID, used to find/remove it later
+		if ( !handler.guid ) {
+			handler.guid = jQuery.guid++;
+		}
+
+		// Init the element's event structure and main handler, if this is the first
+		if ( !(events = elemData.events) ) {
+			events = elemData.events = {};
+		}
+		if ( !(eventHandle = elemData.handle) ) {
+			eventHandle = elemData.handle = function( e ) {
+				// Discard the second event of a jQuery.event.trigger() and
+				// when an event is called after a page has unloaded
+				return typeof jQuery !== strundefined && (!e || jQuery.event.triggered !== e.type) ?
+					jQuery.event.dispatch.apply( eventHandle.elem, arguments ) :
+					undefined;
+			};
+			// Add elem as a property of the handle fn to prevent a memory leak with IE non-native events
+			eventHandle.elem = elem;
+		}
+
+		// Handle multiple events separated by a space
+		types = ( types || "" ).match( rnotwhite ) || [ "" ];
+		t = types.length;
+		while ( t-- ) {
+			tmp = rtypenamespace.exec( types[t] ) || [];
+			type = origType = tmp[1];
+			namespaces = ( tmp[2] || "" ).split( "." ).sort();
+
+			// There *must* be a type, no attaching namespace-only handlers
+			if ( !type ) {
+				continue;
+			}
+
+			// If event changes its type, use the special event handlers for the changed type
+			special = jQuery.event.special[ type ] || {};
+
+			// If selector defined, determine special event api type, otherwise given type
+			type = ( selector ? special.delegateType : special.bindType ) || type;
+
+			// Update special based on newly reset type
+			special = jQuery.event.special[ type ] || {};
+
+			// handleObj is passed to all event handlers
+			handleObj = jQuery.extend({
+				type: type,
+				origType: origType,
+				data: data,
+				handler: handler,
+				guid: handler.guid,
+				selector: selector,
+				needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
+				namespace: namespaces.join(".")
+			}, handleObjIn );
+
+			// Init the event handler queue if we're the first
+			if ( !(handlers = events[ type ]) ) {
+				handlers = events[ type ] = [];
+				handlers.delegateCount = 0;
+
+				// Only use addEventListener/attachEvent if the special events handler returns false
+				if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
+					// Bind the global event handler to the element
+					if ( elem.addEventListener ) {
+						elem.addEventListener( type, eventHandle, false );
+
+					} else if ( elem.attachEvent ) {
+						elem.attachEvent( "on" + type, eventHandle );
+					}
+				}
+			}
+
+			if ( special.add ) {
+				special.add.call( elem, handleObj );
+
+				if ( !handleObj.handler.guid ) {
+					handleObj.handler.guid = handler.guid;
+				}
+			}
+
+			// Add to the element's handler list, delegates in front
+			if ( selector ) {
+				handlers.splice( handlers.delegateCount++, 0, handleObj );
+			} else {
+				handlers.push( handleObj );
+			}
+
+			// Keep track of which events have ever been used, for event optimization
+			jQuery.event.global[ type ] = true;
+		}
+
+		// Nullify elem to prevent memory leaks in IE
+		elem = null;
+	},
+
+	// Detach an event or set of events from an element
+	remove: function( elem, types, handler, selector, mappedTypes ) {
+		var j, handleObj, tmp,
+			origCount, t, events,
+			special, handlers, type,
+			namespaces, origType,
+			elemData = jQuery.hasData( elem ) && jQuery._data( elem );
+
+		if ( !elemData || !(events = elemData.events) ) {
+			return;
+		}
+
+		// Once for each type.namespace in types; type may be omitted
+		types = ( types || "" ).match( rnotwhite ) || [ "" ];
+		t = types.length;
+		while ( t-- ) {
+			tmp = rtypenamespace.exec( types[t] ) || [];
+			type = origType = tmp[1];
+			namespaces = ( tmp[2] || "" ).split( "." ).sort();
+
+			// Unbind all events (on this namespace, if provided) for the element
+			if ( !type ) {
+				for ( type in events ) {
+					jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
+				}
+				continue;
+			}
+
+			special = jQuery.event.special[ type ] || {};
+			type = ( selector ? special.delegateType : special.bindType ) || type;
+			handlers = events[ type ] || [];
+			tmp = tmp[2] && new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" );
+
+			// Remove matching events
+			origCount = j = handlers.length;
+			while ( j-- ) {
+				handleObj = handlers[ j ];
+
+				if ( ( mappedTypes || origType === handleObj.origType ) &&
+					( !handler || handler.guid === handleObj.guid ) &&
+					( !tmp || tmp.test( handleObj.namespace ) ) &&
+					( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) {
+					handlers.splice( j, 1 );
+
+					if ( handleObj.selector ) {
+						handlers.delegateCount--;
+					}
+					if ( special.remove ) {
+						special.remove.call( elem, handleObj );
+					}
+				}
+			}
+
+			// Remove generic event handler if we removed something and no more handlers exist
+			// (avoids potential for endless recursion during removal of special event handlers)
+			if ( origCount && !handlers.length ) {
+				if ( !special.teardown || special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
+					jQuery.removeEvent( elem, type, elemData.handle );
+				}
+
+				delete events[ type ];
+			}
+		}
+
+		// Remove the expando if it's no longer used
+		if ( jQuery.isEmptyObject( events ) ) {
+			delete elemData.handle;
+
+			// removeData also checks for emptiness and clears the expando if empty
+			// so use it instead of delete
+			jQuery._removeData( elem, "events" );
+		}
+	},
+
+	trigger: function( event, data, elem, onlyHandlers ) {
+		var handle, ontype, cur,
+			bubbleType, special, tmp, i,
+			eventPath = [ elem || document ],
+			type = hasOwn.call( event, "type" ) ? event.type : event,
+			namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split(".") : [];
+
+		cur = tmp = elem = elem || document;
+
+		// Don't do events on text and comment nodes
+		if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
+			return;
+		}
+
+		// focus/blur morphs to focusin/out; ensure we're not firing them right now
+		if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
+			return;
+		}
+
+		if ( type.indexOf(".") >= 0 ) {
+			// Namespaced trigger; create a regexp to match event type in handle()
+			namespaces = type.split(".");
+			type = namespaces.shift();
+			namespaces.sort();
+		}
+		ontype = type.indexOf(":") < 0 && "on" + type;
+
+		// Caller can pass in a jQuery.Event object, Object, or just an event type string
+		event = event[ jQuery.expando ] ?
+			event :
+			new jQuery.Event( type, typeof event === "object" && event );
+
+		// Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true)
+		event.isTrigger = onlyHandlers ? 2 : 3;
+		event.namespace = namespaces.join(".");
+		event.namespace_re = event.namespace ?
+			new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" ) :
+			null;
+
+		// Clean up the event in case it is being reused
+		event.result = undefined;
+		if ( !event.target ) {
+			event.target = elem;
+		}
+
+		// Clone any incoming data and prepend the event, creating the handler arg list
+		data = data == null ?
+			[ event ] :
+			jQuery.makeArray( data, [ event ] );
+
+		// Allow special events to draw outside the lines
+		special = jQuery.event.special[ type ] || {};
+		if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
+			return;
+		}
+
+		// Determine event propagation path in advance, per W3C events spec (#9951)
+		// Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
+		if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) {
+
+			bubbleType = special.delegateType || type;
+			if ( !rfocusMorph.test( bubbleType + type ) ) {
+				cur = cur.parentNode;
+			}
+			for ( ; cur; cur = cur.parentNode ) {
+				eventPath.push( cur );
+				tmp = cur;
+			}
+
+			// Only add window if we got to document (e.g., not plain obj or detached DOM)
+			if ( tmp === (elem.ownerDocument || document) ) {
+				eventPath.push( tmp.defaultView || tmp.parentWindow || window );
+			}
+		}
+
+		// Fire handlers on the event path
+		i = 0;
+		while ( (cur = eventPath[i++]) && !event.isPropagationStopped() ) {
+
+			event.type = i > 1 ?
+				bubbleType :
+				special.bindType || type;
+
+			// jQuery handler
+			handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" );
+			if ( handle ) {
+				handle.apply( cur, data );
+			}
+
+			// Native handler
+			handle = ontype && cur[ ontype ];
+			if ( handle && handle.apply && jQuery.acceptData( cur ) ) {
+				event.result = handle.apply( cur, data );
+				if ( event.result === false ) {
+					event.preventDefault();
+				}
+			}
+		}
+		event.type = type;
+
+		// If nobody prevented the default action, do it now
+		if ( !onlyHandlers && !event.isDefaultPrevented() ) {
+
+			if ( (!special._default || special._default.apply( eventPath.pop(), data ) === false) &&
+				jQuery.acceptData( elem ) ) {
+
+				// Call a native DOM method on the target with the same name name as the event.
+				// Can't use an .isFunction() check here because IE6/7 fails that test.
+				// Don't do default actions on window, that's where global variables be (#6170)
+				if ( ontype && elem[ type ] && !jQuery.isWindow( elem ) ) {
+
+					// Don't re-trigger an onFOO event when we call its FOO() method
+					tmp = elem[ ontype ];
+
+					if ( tmp ) {
+						elem[ ontype ] = null;
+					}
+
+					// Prevent re-triggering of the same event, since we already bubbled it above
+					jQuery.event.triggered = type;
+					try {
+						elem[ type ]();
+					} catch ( e ) {
+						// IE<9 dies on focus/blur to hidden element (#1486,#12518)
+						// only reproducible on winXP IE8 native, not IE9 in IE8 mode
+					}
+					jQuery.event.triggered = undefined;
+
+					if ( tmp ) {
+						elem[ ontype ] = tmp;
+					}
+				}
+			}
+		}
+
+		return event.result;
+	},
+
+	dispatch: function( event ) {
+
+		// Make a writable jQuery.Event from the native event object
+		event = jQuery.event.fix( event );
+
+		var i, ret, handleObj, matched, j,
+			handlerQueue = [],
+			args = slice.call( arguments ),
+			handlers = ( jQuery._data( this, "events" ) || {} )[ event.type ] || [],
+			special = jQuery.event.special[ event.type ] || {};
+
+		// Use the fix-ed jQuery.Event rather than the (read-only) native event
+		args[0] = event;
+		event.delegateTarget = this;
+
+		// Call the preDispatch hook for the mapped type, and let it bail if desired
+		if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
+			return;
+		}
+
+		// Determine handlers
+		handlerQueue = jQuery.event.handlers.call( this, event, handlers );
+
+		// Run delegates first; they may want to stop propagation beneath us
+		i = 0;
+		while ( (matched = handlerQueue[ i++ ]) && !event.isPropagationStopped() ) {
+			event.currentTarget = matched.elem;
+
+			j = 0;
+			while ( (handleObj = matched.handlers[ j++ ]) && !event.isImmediatePropagationStopped() ) {
+
+				// Triggered event must either 1) have no namespace, or
+				// 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace).
+				if ( !event.namespace_re || event.namespace_re.test( handleObj.namespace ) ) {
+
+					event.handleObj = handleObj;
+					event.data = handleObj.data;
+
+					ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler )
+							.apply( matched.elem, args );
+
+					if ( ret !== undefined ) {
+						if ( (event.result = ret) === false ) {
+							event.preventDefault();
+							event.stopPropagation();
+						}
+					}
+				}
+			}
+		}
+
+		// Call the postDispatch hook for the mapped type
+		if ( special.postDispatch ) {
+			special.postDispatch.call( this, event );
+		}
+
+		return event.result;
+	},
+
+	handlers: function( event, handlers ) {
+		var sel, handleObj, matches, i,
+			handlerQueue = [],
+			delegateCount = handlers.delegateCount,
+			cur = event.target;
+
+		// Find delegate handlers
+		// Black-hole SVG <use> instance trees (#13180)
+		// Avoid non-left-click bubbling in Firefox (#3861)
+		if ( delegateCount && cur.nodeType && (!event.button || event.type !== "click") ) {
+
+			/* jshint eqeqeq: false */
+			for ( ; cur != this; cur = cur.parentNode || this ) {
+				/* jshint eqeqeq: true */
+
+				// Don't check non-elements (#13208)
+				// Don't process clicks on disabled elements (#6911, #8165, #11382, #11764)
+				if ( cur.nodeType === 1 && (cur.disabled !== true || event.type !== "click") ) {
+					matches = [];
+					for ( i = 0; i < delegateCount; i++ ) {
+						handleObj = handlers[ i ];
+
+						// Don't conflict with Object.prototype properties (#13203)
+						sel = handleObj.selector + " ";
+
+						if ( matches[ sel ] === undefined ) {
+							matches[ sel ] = handleObj.needsContext ?
+								jQuery( sel, this ).index( cur ) >= 0 :
+								jQuery.find( sel, this, null, [ cur ] ).length;
+						}
+						if ( matches[ sel ] ) {
+							matches.push( handleObj );
+						}
+					}
+					if ( matches.length ) {
+						handlerQueue.push({ elem: cur, handlers: matches });
+					}
+				}
+			}
+		}
+
+		// Add the remaining (directly-bound) handlers
+		if ( delegateCount < handlers.length ) {
+			handlerQueue.push({ elem: this, handlers: handlers.slice( delegateCount ) });
+		}
+
+		return handlerQueue;
+	},
+
+	fix: function( event ) {
+		if ( event[ jQuery.expando ] ) {
+			return event;
+		}
+
+		// Create a writable copy of the event object and normalize some properties
+		var i, prop, copy,
+			type = event.type,
+			originalEvent = event,
+			fixHook = this.fixHooks[ type ];
+
+		if ( !fixHook ) {
+			this.fixHooks[ type ] = fixHook =
+				rmouseEvent.test( type ) ? this.mouseHooks :
+				rkeyEvent.test( type ) ? this.keyHooks :
+				{};
+		}
+		copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props;
+
+		event = new jQuery.Event( originalEvent );
+
+		i = copy.length;
+		while ( i-- ) {
+			prop = copy[ i ];
+			event[ prop ] = originalEvent[ prop ];
+		}
+
+		// Support: IE<9
+		// Fix target property (#1925)
+		if ( !event.target ) {
+			event.target = originalEvent.srcElement || document;
+		}
+
+		// Support: Chrome 23+, Safari?
+		// Target should not be a text node (#504, #13143)
+		if ( event.target.nodeType === 3 ) {
+			event.target = event.target.parentNode;
+		}
+
+		// Support: IE<9
+		// For mouse/key events, metaKey==false if it's undefined (#3368, #11328)
+		event.metaKey = !!event.metaKey;
+
+		return fixHook.filter ? fixHook.filter( event, originalEvent ) : event;
+	},
+
+	// Includes some event props shared by KeyEvent and MouseEvent
+	props: "altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "),
+
+	fixHooks: {},
+
+	keyHooks: {
+		props: "char charCode key keyCode".split(" "),
+		filter: function( event, original ) {
+
+			// Add which for key events
+			if ( event.which == null ) {
+				event.which = original.charCode != null ? original.charCode : original.keyCode;
+			}
+
+			return event;
+		}
+	},
+
+	mouseHooks: {
+		props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "),
+		filter: function( event, original ) {
+			var body, eventDoc, doc,
+				button = original.button,
+				fromElement = original.fromElement;
+
+			// Calculate pageX/Y if missing and clientX/Y available
+			if ( event.pageX == null && original.clientX != null ) {
+				eventDoc = event.target.ownerDocument || document;
+				doc = eventDoc.documentElement;
+				body = eventDoc.body;
+
+				event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 );
+				event.pageY = original.clientY + ( doc && doc.scrollTop  || body && body.scrollTop  || 0 ) - ( doc && doc.clientTop  || body && body.clientTop  || 0 );
+			}
+
+			// Add relatedTarget, if necessary
+			if ( !event.relatedTarget && fromElement ) {
+				event.relatedTarget = fromElement === event.target ? original.toElement : fromElement;
+			}
+
+			// Add which for click: 1 === left; 2 === middle; 3 === right
+			// Note: button is not normalized, so don't use it
+			if ( !event.which && button !== undefined ) {
+				event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) );
+			}
+
+			return event;
+		}
+	},
+
+	special: {
+		load: {
+			// Prevent triggered image.load events from bubbling to window.load
+			noBubble: true
+		},
+		focus: {
+			// Fire native event if possible so blur/focus sequence is correct
+			trigger: function() {
+				if ( this !== safeActiveElement() && this.focus ) {
+					try {
+						this.focus();
+						return false;
+					} catch ( e ) {
+						// Support: IE<9
+						// If we error on focus to hidden element (#1486, #12518),
+						// let .trigger() run the handlers
+					}
+				}
+			},
+			delegateType: "focusin"
+		},
+		blur: {
+			trigger: function() {
+				if ( this === safeActiveElement() && this.blur ) {
+					this.blur();
+					return false;
+				}
+			},
+			delegateType: "focusout"
+		},
+		click: {
+			// For checkbox, fire native event so checked state will be right
+			trigger: function() {
+				if ( jQuery.nodeName( this, "input" ) && this.type === "checkbox" && this.click ) {
+					this.click();
+					return false;
+				}
+			},
+
+			// For cross-browser consistency, don't fire native .click() on links
+			_default: function( event ) {
+				return jQuery.nodeName( event.target, "a" );
+			}
+		},
+
+		beforeunload: {
+			postDispatch: function( event ) {
+
+				// Support: Firefox 20+
+				// Firefox doesn't alert if the returnValue field is not set.
+				if ( event.result !== undefined && event.originalEvent ) {
+					event.originalEvent.returnValue = event.result;
+				}
+			}
+		}
+	},
+
+	simulate: function( type, elem, event, bubble ) {
+		// Piggyback on a donor event to simulate a different one.
+		// Fake originalEvent to avoid donor's stopPropagation, but if the
+		// simulated event prevents default then we do the same on the donor.
+		var e = jQuery.extend(
+			new jQuery.Event(),
+			event,
+			{
+				type: type,
+				isSimulated: true,
+				originalEvent: {}
+			}
+		);
+		if ( bubble ) {
+			jQuery.event.trigger( e, null, elem );
+		} else {
+			jQuery.event.dispatch.call( elem, e );
+		}
+		if ( e.isDefaultPrevented() ) {
+			event.preventDefault();
+		}
+	}
+};
+
+jQuery.removeEvent = document.removeEventListener ?
+	function( elem, type, handle ) {
+		if ( elem.removeEventListener ) {
+			elem.removeEventListener( type, handle, false );
+		}
+	} :
+	function( elem, type, handle ) {
+		var name = "on" + type;
+
+		if ( elem.detachEvent ) {
+
+			// #8545, #7054, preventing memory leaks for custom events in IE6-8
+			// detachEvent needed property on element, by name of that event, to properly expose it to GC
+			if ( typeof elem[ name ] === strundefined ) {
+				elem[ name ] = null;
+			}
+
+			elem.detachEvent( name, handle );
+		}
+	};
+
+jQuery.Event = function( src, props ) {
+	// Allow instantiation without the 'new' keyword
+	if ( !(this instanceof jQuery.Event) ) {
+		return new jQuery.Event( src, props );
+	}
+
+	// Event object
+	if ( src && src.type ) {
+		this.originalEvent = src;
+		this.type = src.type;
+
+		// Events bubbling up the document may have been marked as prevented
+		// by a handler lower down the tree; reflect the correct value.
+		this.isDefaultPrevented = src.defaultPrevented ||
+				src.defaultPrevented === undefined &&
+				// Support: IE < 9, Android < 4.0
+				src.returnValue === false ?
+			returnTrue :
+			returnFalse;
+
+	// Event type
+	} else {
+		this.type = src;
+	}
+
+	// Put explicitly provided properties onto the event object
+	if ( props ) {
+		jQuery.extend( this, props );
+	}
+
+	// Create a timestamp if incoming event doesn't have one
+	this.timeStamp = src && src.timeStamp || jQuery.now();
+
+	// Mark it as fixed
+	this[ jQuery.expando ] = true;
+};
+
+// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
+// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
+jQuery.Event.prototype = {
+	isDefaultPrevented: returnFalse,
+	isPropagationStopped: returnFalse,
+	isImmediatePropagationStopped: returnFalse,
+
+	preventDefault: function() {
+		var e = this.originalEvent;
+
+		this.isDefaultPrevented = returnTrue;
+		if ( !e ) {
+			return;
+		}
+
+		// If preventDefault exists, run it on the original event
+		if ( e.preventDefault ) {
+			e.preventDefault();
+
+		// Support: IE
+		// Otherwise set the returnValue property of the original event to false
+		} else {
+			e.returnValue = false;
+		}
+	},
+	stopPropagation: function() {
+		var e = this.originalEvent;
+
+		this.isPropagationStopped = returnTrue;
+		if ( !e ) {
+			return;
+		}
+		// If stopPropagation exists, run it on the original event
+		if ( e.stopPropagation ) {
+			e.stopPropagation();
+		}
+
+		// Support: IE
+		// Set the cancelBubble property of the original event to true
+		e.cancelBubble = true;
+	},
+	stopImmediatePropagation: function() {
+		var e = this.originalEvent;
+
+		this.isImmediatePropagationStopped = returnTrue;
+
+		if ( e && e.stopImmediatePropagation ) {
+			e.stopImmediatePropagation();
+		}
+
+		this.stopPropagation();
+	}
+};
+
+// Create mouseenter/leave events using mouseover/out and event-time checks
+jQuery.each({
+	mouseenter: "mouseover",
+	mouseleave: "mouseout",
+	pointerenter: "pointerover",
+	pointerleave: "pointerout"
+}, function( orig, fix ) {
+	jQuery.event.special[ orig ] = {
+		delegateType: fix,
+		bindType: fix,
+
+		handle: function( event ) {
+			var ret,
+				target = this,
+				related = event.relatedTarget,
+				handleObj = event.handleObj;
+
+			// For mousenter/leave call the handler if related is outside the target.
+			// NB: No relatedTarget if the mouse left/entered the browser window
+			if ( !related || (related !== target && !jQuery.contains( target, related )) ) {
+				event.type = handleObj.origType;
+				ret = handleObj.handler.apply( this, arguments );
+				event.type = fix;
+			}
+			return ret;
+		}
+	};
+});
+
+// IE submit delegation
+if ( !support.submitBubbles ) {
+
+	jQuery.event.special.submit = {
+		setup: function() {
+			// Only need this for delegated form submit events
+			if ( jQuery.nodeName( this, "form" ) ) {
+				return false;
+			}
+
+			// Lazy-add a submit handler when a descendant form may potentially be submitted
+			jQuery.event.add( this, "click._submit keypress._submit", function( e ) {
+				// Node name check avoids a VML-related crash in IE (#9807)
+				var elem = e.target,
+					form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined;
+				if ( form && !jQuery._data( form, "submitBubbles" ) ) {
+					jQuery.event.add( form, "submit._submit", function( event ) {
+						event._submit_bubble = true;
+					});
+					jQuery._data( form, "submitBubbles", true );
+				}
+			});
+			// return undefined since we don't need an event listener
+		},
+
+		postDispatch: function( event ) {
+			// If form was submitted by the user, bubble the event up the tree
+			if ( event._submit_bubble ) {
+				delete event._submit_bubble;
+				if ( this.parentNode && !event.isTrigger ) {
+					jQuery.event.simulate( "submit", this.parentNode, event, true );
+				}
+			}
+		},
+
+		teardown: function() {
+			// Only need this for delegated form submit events
+			if ( jQuery.nodeName( this, "form" ) ) {
+				return false;
+			}
+
+			// Remove delegated handlers; cleanData eventually reaps submit handlers attached above
+			jQuery.event.remove( this, "._submit" );
+		}
+	};
+}
+
+// IE change delegation and checkbox/radio fix
+if ( !support.changeBubbles ) {
+
+	jQuery.event.special.change = {
+
+		setup: function() {
+
+			if ( rformElems.test( this.nodeName ) ) {
+				// IE doesn't fire change on a check/radio until blur; trigger it on click
+				// after a propertychange. Eat the blur-change in special.change.handle.
+				// This still fires onchange a second time for check/radio after blur.
+				if ( this.type === "checkbox" || this.type === "radio" ) {
+					jQuery.event.add( this, "propertychange._change", function( event ) {
+						if ( event.originalEvent.propertyName === "checked" ) {
+							this._just_changed = true;
+						}
+					});
+					jQuery.event.add( this, "click._change", function( event ) {
+						if ( this._just_changed && !event.isTrigger ) {
+							this._just_changed = false;
+						}
+						// Allow triggered, simulated change events (#11500)
+						jQuery.event.simulate( "change", this, event, true );
+					});
+				}
+				return false;
+			}
+			// Delegated event; lazy-add a change handler on descendant inputs
+			jQuery.event.add( this, "beforeactivate._change", function( e ) {
+				var elem = e.target;
+
+				if ( rformElems.test( elem.nodeName ) && !jQuery._data( elem, "changeBubbles" ) ) {
+					jQuery.event.add( elem, "change._change", function( event ) {
+						if ( this.parentNode && !event.isSimulated && !event.isTrigger ) {
+							jQuery.event.simulate( "change", this.parentNode, event, true );
+						}
+					});
+					jQuery._data( elem, "changeBubbles", true );
+				}
+			});
+		},
+
+		handle: function( event ) {
+			var elem = event.target;
+
+			// Swallow native change events from checkbox/radio, we already triggered them above
+			if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) {
+				return event.handleObj.handler.apply( this, arguments );
+			}
+		},
+
+		teardown: function() {
+			jQuery.event.remove( this, "._change" );
+
+			return !rformElems.test( this.nodeName );
+		}
+	};
+}
+
+// Create "bubbling" focus and blur events
+if ( !support.focusinBubbles ) {
+	jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) {
+
+		// Attach a single capturing handler on the document while someone wants focusin/focusout
+		var handler = function( event ) {
+				jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true );
+			};
+
+		jQuery.event.special[ fix ] = {
+			setup: function() {
+				var doc = this.ownerDocument || this,
+					attaches = jQuery._data( doc, fix );
+
+				if ( !attaches ) {
+					doc.addEventListener( orig, handler, true );
+				}
+				jQuery._data( doc, fix, ( attaches || 0 ) + 1 );
+			},
+			teardown: function() {
+				var doc = this.ownerDocument || this,
+					attaches = jQuery._data( doc, fix ) - 1;
+
+				if ( !attaches ) {
+					doc.removeEventListener( orig, handler, true );
+					jQuery._removeData( doc, fix );
+				} else {
+					jQuery._data( doc, fix, attaches );
+				}
+			}
+		};
+	});
+}
+
+jQuery.fn.extend({
+
+	on: function( types, selector, data, fn, /*INTERNAL*/ one ) {
+		var type, origFn;
+
+		// Types can be a map of types/handlers
+		if ( typeof types === "object" ) {
+			// ( types-Object, selector, data )
+			if ( typeof selector !== "string" ) {
+				// ( types-Object, data )
+				data = data || selector;
+				selector = undefined;
+			}
+			for ( type in types ) {
+				this.on( type, selector, data, types[ type ], one );
+			}
+			return this;
+		}
+
+		if ( data == null && fn == null ) {
+			// ( types, fn )
+			fn = selector;
+			data = selector = undefined;
+		} else if ( fn == null ) {
+			if ( typeof selector === "string" ) {
+				// ( types, selector, fn )
+				fn = data;
+				data = undefined;
+			} else {
+				// ( types, data, fn )
+				fn = data;
+				data = selector;
+				selector = undefined;
+			}
+		}
+		if ( fn === false ) {
+			fn = returnFalse;
+		} else if ( !fn ) {
+			return this;
+		}
+
+		if ( one === 1 ) {
+			origFn = fn;
+			fn = function( event ) {
+				// Can use an empty set, since event contains the info
+				jQuery().off( event );
+				return origFn.apply( this, arguments );
+			};
+			// Use same guid so caller can remove using origFn
+			fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
+		}
+		return this.each( function() {
+			jQuery.event.add( this, types, fn, data, selector );
+		});
+	},
+	one: function( types, selector, data, fn ) {
+		return this.on( types, selector, data, fn, 1 );
+	},
+	off: function( types, selector, fn ) {
+		var handleObj, type;
+		if ( types && types.preventDefault && types.handleObj ) {
+			// ( event )  dispatched jQuery.Event
+			handleObj = types.handleObj;
+			jQuery( types.delegateTarget ).off(
+				handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType,
+				handleObj.selector,
+				handleObj.handler
+			);
+			return this;
+		}
+		if ( typeof types === "object" ) {
+			// ( types-object [, selector] )
+			for ( type in types ) {
+				this.off( type, selector, types[ type ] );
+			}
+			return this;
+		}
+		if ( selector === false || typeof selector === "function" ) {
+			// ( types [, fn] )
+			fn = selector;
+			selector = undefined;
+		}
+		if ( fn === false ) {
+			fn = returnFalse;
+		}
+		return this.each(function() {
+			jQuery.event.remove( this, types, fn, selector );
+		});
+	},
+
+	trigger: function( type, data ) {
+		return this.each(function() {
+			jQuery.event.trigger( type, data, this );
+		});
+	},
+	triggerHandler: function( type, data ) {
+		var elem = this[0];
+		if ( elem ) {
+			return jQuery.event.trigger( type, data, elem, true );
+		}
+	}
+});
+
+
+function createSafeFragment( document ) {
+	var list = nodeNames.split( "|" ),
+		safeFrag = document.createDocumentFragment();
+
+	if ( safeFrag.createElement ) {
+		while ( list.length ) {
+			safeFrag.createElement(
+				list.pop()
+			);
+		}
+	}
+	return safeFrag;
+}
+
+var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" +
+		"header|hgroup|mark|meter|nav|output|progress|section|summary|time|video",
+	rinlinejQuery = / jQuery\d+="(?:null|\d+)"/g,
+	rnoshimcache = new RegExp("<(?:" + nodeNames + ")[\\s/>]", "i"),
+	rleadingWhitespace = /^\s+/,
+	rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/gi,
+	rtagName = /<([\w:]+)/,
+	rtbody = /<tbody/i,
+	rhtml = /<|&#?\w+;/,
+	rnoInnerhtml = /<(?:script|style|link)/i,
+	// checked="checked" or checked
+	rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
+	rscriptType = /^$|\/(?:java|ecma)script/i,
+	rscriptTypeMasked = /^true\/(.*)/,
+	rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g,
+
+	// We have to close these tags to support XHTML (#13200)
+	wrapMap = {
+		option: [ 1, "<select multiple='multiple'>", "</select>" ],
+		legend: [ 1, "<fieldset>", "</fieldset>" ],
+		area: [ 1, "<map>", "</map>" ],
+		param: [ 1, "<object>", "</object>" ],
+		thead: [ 1, "<table>", "</table>" ],
+		tr: [ 2, "<table><tbody>", "</tbody></table>" ],
+		col: [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ],
+		td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
+
+		// IE6-8 can't serialize link, script, style, or any html5 (NoScope) tags,
+		// unless wrapped in a div with non-breaking characters in front of it.
+		_default: support.htmlSerialize ? [ 0, "", "" ] : [ 1, "X<div>", "</div>"  ]
+	},
+	safeFragment = createSafeFragment( document ),
+	fragmentDiv = safeFragment.appendChild( document.createElement("div") );
+
+wrapMap.optgroup = wrapMap.option;
+wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
+wrapMap.th = wrapMap.td;
+
+function getAll( context, tag ) {
+	var elems, elem,
+		i = 0,
+		found = typeof context.getElementsByTagName !== strundefined ? context.getElementsByTagName( tag || "*" ) :
+			typeof context.querySelectorAll !== strundefined ? context.querySelectorAll( tag || "*" ) :
+			undefined;
+
+	if ( !found ) {
+		for ( found = [], elems = context.childNodes || context; (elem = elems[i]) != null; i++ ) {
+			if ( !tag || jQuery.nodeName( elem, tag ) ) {
+				found.push( elem );
+			} else {
+				jQuery.merge( found, getAll( elem, tag ) );
+			}
+		}
+	}
+
+	return tag === undefined || tag && jQuery.nodeName( context, tag ) ?
+		jQuery.merge( [ context ], found ) :
+		found;
+}
+
+// Used in buildFragment, fixes the defaultChecked property
+function fixDefaultChecked( elem ) {
+	if ( rcheckableType.test( elem.type ) ) {
+		elem.defaultChecked = elem.checked;
+	}
+}
+
+// Support: IE<8
+// Manipulating tables requires a tbody
+function manipulationTarget( elem, content ) {
+	return jQuery.nodeName( elem, "table" ) &&
+		jQuery.nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ?
+
+		elem.getElementsByTagName("tbody")[0] ||
+			elem.appendChild( elem.ownerDocument.createElement("tbody") ) :
+		elem;
+}
+
+// Replace/restore the type attribute of script elements for safe DOM manipulation
+function disableScript( elem ) {
+	elem.type = (jQuery.find.attr( elem, "type" ) !== null) + "/" + elem.type;
+	return elem;
+}
+function restoreScript( elem ) {
+	var match = rscriptTypeMasked.exec( elem.type );
+	if ( match ) {
+		elem.type = match[1];
+	} else {
+		elem.removeAttribute("type");
+	}
+	return elem;
+}
+
+// Mark scripts as having already been evaluated
+function setGlobalEval( elems, refElements ) {
+	var elem,
+		i = 0;
+	for ( ; (elem = elems[i]) != null; i++ ) {
+		jQuery._data( elem, "globalEval", !refElements || jQuery._data( refElements[i], "globalEval" ) );
+	}
+}
+
+function cloneCopyEvent( src, dest ) {
+
+	if ( dest.nodeType !== 1 || !jQuery.hasData( src ) ) {
+		return;
+	}
+
+	var type, i, l,
+		oldData = jQuery._data( src ),
+		curData = jQuery._data( dest, oldData ),
+		events = oldData.events;
+
+	if ( events ) {
+		delete curData.handle;
+		curData.events = {};
+
+		for ( type in events ) {
+			for ( i = 0, l = events[ type ].length; i < l; i++ ) {
+				jQuery.event.add( dest, type, events[ type ][ i ] );
+			}
+		}
+	}
+
+	// make the cloned public data object a copy from the original
+	if ( curData.data ) {
+		curData.data = jQuery.extend( {}, curData.data );
+	}
+}
+
+function fixCloneNodeIssues( src, dest ) {
+	var nodeName, e, data;
+
+	// We do not need to do anything for non-Elements
+	if ( dest.nodeType !== 1 ) {
+		return;
+	}
+
+	nodeName = dest.nodeName.toLowerCase();
+
+	// IE6-8 copies events bound via attachEvent when using cloneNode.
+	if ( !support.noCloneEvent && dest[ jQuery.expando ] ) {
+		data = jQuery._data( dest );
+
+		for ( e in data.events ) {
+			jQuery.removeEvent( dest, e, data.handle );
+		}
+
+		// Event data gets referenced instead of copied if the expando gets copied too
+		dest.removeAttribute( jQuery.expando );
+	}
+
+	// IE blanks contents when cloning scripts, and tries to evaluate newly-set text
+	if ( nodeName === "script" && dest.text !== src.text ) {
+		disableScript( dest ).text = src.text;
+		restoreScript( dest );
+
+	// IE6-10 improperly clones children of object elements using classid.
+	// IE10 throws NoModificationAllowedError if parent is null, #12132.
+	} else if ( nodeName === "object" ) {
+		if ( dest.parentNode ) {
+			dest.outerHTML = src.outerHTML;
+		}
+
+		// This path appears unavoidable for IE9. When cloning an object
+		// element in IE9, the outerHTML strategy above is not sufficient.
+		// If the src has innerHTML and the destination does not,
+		// copy the src.innerHTML into the dest.innerHTML. #10324
+		if ( support.html5Clone && ( src.innerHTML && !jQuery.trim(dest.innerHTML) ) ) {
+			dest.innerHTML = src.innerHTML;
+		}
+
+	} else if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
+		// IE6-8 fails to persist the checked state of a cloned checkbox
+		// or radio button. Worse, IE6-7 fail to give the cloned element
+		// a checked appearance if the defaultChecked value isn't also set
+
+		dest.defaultChecked = dest.checked = src.checked;
+
+		// IE6-7 get confused and end up setting the value of a cloned
+		// checkbox/radio button to an empty string instead of "on"
+		if ( dest.value !== src.value ) {
+			dest.value = src.value;
+		}
+
+	// IE6-8 fails to return the selected option to the default selected
+	// state when cloning options
+	} else if ( nodeName === "option" ) {
+		dest.defaultSelected = dest.selected = src.defaultSelected;
+
+	// IE6-8 fails to set the defaultValue to the correct value when
+	// cloning other types of input fields
+	} else if ( nodeName === "input" || nodeName === "textarea" ) {
+		dest.defaultValue = src.defaultValue;
+	}
+}
+
+jQuery.extend({
+	clone: function( elem, dataAndEvents, deepDataAndEvents ) {
+		var destElements, node, clone, i, srcElements,
+			inPage = jQuery.contains( elem.ownerDocument, elem );
+
+		if ( support.html5Clone || jQuery.isXMLDoc(elem) || !rnoshimcache.test( "<" + elem.nodeName + ">" ) ) {
+			clone = elem.cloneNode( true );
+
+		// IE<=8 does not properly clone detached, unknown element nodes
+		} else {
+			fragmentDiv.innerHTML = elem.outerHTML;
+			fragmentDiv.removeChild( clone = fragmentDiv.firstChild );
+		}
+
+		if ( (!support.noCloneEvent || !support.noCloneChecked) &&
+				(elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) {
+
+			// We eschew Sizzle here for performance reasons: http://jsperf.com/getall-vs-sizzle/2
+			destElements = getAll( clone );
+			srcElements = getAll( elem );
+
+			// Fix all IE cloning issues
+			for ( i = 0; (node = srcElements[i]) != null; ++i ) {
+				// Ensure that the destination node is not null; Fixes #9587
+				if ( destElements[i] ) {
+					fixCloneNodeIssues( node, destElements[i] );
+				}
+			}
+		}
+
+		// Copy the events from the original to the clone
+		if ( dataAndEvents ) {
+			if ( deepDataAndEvents ) {
+				srcElements = srcElements || getAll( elem );
+				destElements = destElements || getAll( clone );
+
+				for ( i = 0; (node = srcElements[i]) != null; i++ ) {
+					cloneCopyEvent( node, destElements[i] );
+				}
+			} else {
+				cloneCopyEvent( elem, clone );
+			}
+		}
+
+		// Preserve script evaluation history
+		destElements = getAll( clone, "script" );
+		if ( destElements.length > 0 ) {
+			setGlobalEval( destElements, !inPage && getAll( elem, "script" ) );
+		}
+
+		destElements = srcElements = node = null;
+
+		// Return the cloned set
+		return clone;
+	},
+
+	buildFragment: function( elems, context, scripts, selection ) {
+		var j, elem, contains,
+			tmp, tag, tbody, wrap,
+			l = elems.length,
+
+			// Ensure a safe fragment
+			safe = createSafeFragment( context ),
+
+			nodes = [],
+			i = 0;
+
+		for ( ; i < l; i++ ) {
+			elem = elems[ i ];
+
+			if ( elem || elem === 0 ) {
+
+				// Add nodes directly
+				if ( jQuery.type( elem ) === "object" ) {
+					jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem );
+
+				// Convert non-html into a text node
+				} else if ( !rhtml.test( elem ) ) {
+					nodes.push( context.createTextNode( elem ) );
+
+				// Convert html into DOM nodes
+				} else {
+					tmp = tmp || safe.appendChild( context.createElement("div") );
+
+					// Deserialize a standard representation
+					tag = (rtagName.exec( elem ) || [ "", "" ])[ 1 ].toLowerCase();
+					wrap = wrapMap[ tag ] || wrapMap._default;
+
+					tmp.innerHTML = wrap[1] + elem.replace( rxhtmlTag, "<$1></$2>" ) + wrap[2];
+
+					// Descend through wrappers to the right content
+					j = wrap[0];
+					while ( j-- ) {
+						tmp = tmp.lastChild;
+					}
+
+					// Manually add leading whitespace removed by IE
+					if ( !support.leadingWhitespace && rleadingWhitespace.test( elem ) ) {
+						nodes.push( context.createTextNode( rleadingWhitespace.exec( elem )[0] ) );
+					}
+
+					// Remove IE's autoinserted <tbody> from table fragments
+					if ( !support.tbody ) {
+
+						// String was a <table>, *may* have spurious <tbody>
+						elem = tag === "table" && !rtbody.test( elem ) ?
+							tmp.firstChild :
+
+							// String was a bare <thead> or <tfoot>
+							wrap[1] === "<table>" && !rtbody.test( elem ) ?
+								tmp :
+								0;
+
+						j = elem && elem.childNodes.length;
+						while ( j-- ) {
+							if ( jQuery.nodeName( (tbody = elem.childNodes[j]), "tbody" ) && !tbody.childNodes.length ) {
+								elem.removeChild( tbody );
+							}
+						}
+					}
+
+					jQuery.merge( nodes, tmp.childNodes );
+
+					// Fix #12392 for WebKit and IE > 9
+					tmp.textContent = "";
+
+					// Fix #12392 for oldIE
+					while ( tmp.firstChild ) {
+						tmp.removeChild( tmp.firstChild );
+					}
+
+					// Remember the top-level container for proper cleanup
+					tmp = safe.lastChild;
+				}
+			}
+		}
+
+		// Fix #11356: Clear elements from fragment
+		if ( tmp ) {
+			safe.removeChild( tmp );
+		}
+
+		// Reset defaultChecked for any radios and checkboxes
+		// about to be appended to the DOM in IE 6/7 (#8060)
+		if ( !support.appendChecked ) {
+			jQuery.grep( getAll( nodes, "input" ), fixDefaultChecked );
+		}
+
+		i = 0;
+		while ( (elem = nodes[ i++ ]) ) {
+
+			// #4087 - If origin and destination elements are the same, and this is
+			// that element, do not do anything
+			if ( selection && jQuery.inArray( elem, selection ) !== -1 ) {
+				continue;
+			}
+
+			contains = jQuery.contains( elem.ownerDocument, elem );
+
+			// Append to fragment
+			tmp = getAll( safe.appendChild( elem ), "script" );
+
+			// Preserve script evaluation history
+			if ( contains ) {
+				setGlobalEval( tmp );
+			}
+
+			// Capture executables
+			if ( scripts ) {
+				j = 0;
+				while ( (elem = tmp[ j++ ]) ) {
+					if ( rscriptType.test( elem.type || "" ) ) {
+						scripts.push( elem );
+					}
+				}
+			}
+		}
+
+		tmp = null;
+
+		return safe;
+	},
+
+	cleanData: function( elems, /* internal */ acceptData ) {
+		var elem, type, id, data,
+			i = 0,
+			internalKey = jQuery.expando,
+			cache = jQuery.cache,
+			deleteExpando = support.deleteExpando,
+			special = jQuery.event.special;
+
+		for ( ; (elem = elems[i]) != null; i++ ) {
+			if ( acceptData || jQuery.acceptData( elem ) ) {
+
+				id = elem[ internalKey ];
+				data = id && cache[ id ];
+
+				if ( data ) {
+					if ( data.events ) {
+						for ( type in data.events ) {
+							if ( special[ type ] ) {
+								jQuery.event.remove( elem, type );
+
+							// This is a shortcut to avoid jQuery.event.remove's overhead
+							} else {
+								jQuery.removeEvent( elem, type, data.handle );
+							}
+						}
+					}
+
+					// Remove cache only if it was not already removed by jQuery.event.remove
+					if ( cache[ id ] ) {
+
+						delete cache[ id ];
+
+						// IE does not allow us to delete expando properties from nodes,
+						// nor does it have a removeAttribute function on Document nodes;
+						// we must handle all of these cases
+						if ( deleteExpando ) {
+							delete elem[ internalKey ];
+
+						} else if ( typeof elem.removeAttribute !== strundefined ) {
+							elem.removeAttribute( internalKey );
+
+						} else {
+							elem[ internalKey ] = null;
+						}
+
+						deletedIds.push( id );
+					}
+				}
+			}
+		}
+	}
+});
+
+jQuery.fn.extend({
+	text: function( value ) {
+		return access( this, function( value ) {
+			return value === undefined ?
+				jQuery.text( this ) :
+				this.empty().append( ( this[0] && this[0].ownerDocument || document ).createTextNode( value ) );
+		}, null, value, arguments.length );
+	},
+
+	append: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+				var target = manipulationTarget( this, elem );
+				target.appendChild( elem );
+			}
+		});
+	},
+
+	prepend: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+				var target = manipulationTarget( this, elem );
+				target.insertBefore( elem, target.firstChild );
+			}
+		});
+	},
+
+	before: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.parentNode ) {
+				this.parentNode.insertBefore( elem, this );
+			}
+		});
+	},
+
+	after: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.parentNode ) {
+				this.parentNode.insertBefore( elem, this.nextSibling );
+			}
+		});
+	},
+
+	remove: function( selector, keepData /* Internal Use Only */ ) {
+		var elem,
+			elems = selector ? jQuery.filter( selector, this ) : this,
+			i = 0;
+
+		for ( ; (elem = elems[i]) != null; i++ ) {
+
+			if ( !keepData && elem.nodeType === 1 ) {
+				jQuery.cleanData( getAll( elem ) );
+			}
+
+			if ( elem.parentNode ) {
+				if ( keepData && jQuery.contains( elem.ownerDocument, elem ) ) {
+					setGlobalEval( getAll( elem, "script" ) );
+				}
+				elem.parentNode.removeChild( elem );
+			}
+		}
+
+		return this;
+	},
+
+	empty: function() {
+		var elem,
+			i = 0;
+
+		for ( ; (elem = this[i]) != null; i++ ) {
+			// Remove element nodes and prevent memory leaks
+			if ( elem.nodeType === 1 ) {
+				jQuery.cleanData( getAll( elem, false ) );
+			}
+
+			// Remove any remaining nodes
+			while ( elem.firstChild ) {
+				elem.removeChild( elem.firstChild );
+			}
+
+			// If this is a select, ensure that it displays empty (#12336)
+			// Support: IE<9
+			if ( elem.options && jQuery.nodeName( elem, "select" ) ) {
+				elem.options.length = 0;
+			}
+		}
+
+		return this;
+	},
+
+	clone: function( dataAndEvents, deepDataAndEvents ) {
+		dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
+		deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
+
+		return this.map(function() {
+			return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
+		});
+	},
+
+	html: function( value ) {
+		return access( this, function( value ) {
+			var elem = this[ 0 ] || {},
+				i = 0,
+				l = this.length;
+
+			if ( value === undefined ) {
+				return elem.nodeType === 1 ?
+					elem.innerHTML.replace( rinlinejQuery, "" ) :
+					undefined;
+			}
+
+			// See if we can take a shortcut and just use innerHTML
+			if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
+				( support.htmlSerialize || !rnoshimcache.test( value )  ) &&
+				( support.leadingWhitespace || !rleadingWhitespace.test( value ) ) &&
+				!wrapMap[ (rtagName.exec( value ) || [ "", "" ])[ 1 ].toLowerCase() ] ) {
+
+				value = value.replace( rxhtmlTag, "<$1></$2>" );
+
+				try {
+					for (; i < l; i++ ) {
+						// Remove element nodes and prevent memory leaks
+						elem = this[i] || {};
+						if ( elem.nodeType === 1 ) {
+							jQuery.cleanData( getAll( elem, false ) );
+							elem.innerHTML = value;
+						}
+					}
+
+					elem = 0;
+
+				// If using innerHTML throws an exception, use the fallback method
+				} catch(e) {}
+			}
+
+			if ( elem ) {
+				this.empty().append( value );
+			}
+		}, null, value, arguments.length );
+	},
+
+	replaceWith: function() {
+		var arg = arguments[ 0 ];
+
+		// Make the changes, replacing each context element with the new content
+		this.domManip( arguments, function( elem ) {
+			arg = this.parentNode;
+
+			jQuery.cleanData( getAll( this ) );
+
+			if ( arg ) {
+				arg.replaceChild( elem, this );
+			}
+		});
+
+		// Force removal if there was no new content (e.g., from empty arguments)
+		return arg && (arg.length || arg.nodeType) ? this : this.remove();
+	},
+
+	detach: function( selector ) {
+		return this.remove( selector, true );
+	},
+
+	domManip: function( args, callback ) {
+
+		// Flatten any nested arrays
+		args = concat.apply( [], args );
+
+		var first, node, hasScripts,
+			scripts, doc, fragment,
+			i = 0,
+			l = this.length,
+			set = this,
+			iNoClone = l - 1,
+			value = args[0],
+			isFunction = jQuery.isFunction( value );
+
+		// We can't cloneNode fragments that contain checked, in WebKit
+		if ( isFunction ||
+				( l > 1 && typeof value === "string" &&
+					!support.checkClone && rchecked.test( value ) ) ) {
+			return this.each(function( index ) {
+				var self = set.eq( index );
+				if ( isFunction ) {
+					args[0] = value.call( this, index, self.html() );
+				}
+				self.domManip( args, callback );
+			});
+		}
+
+		if ( l ) {
+			fragment = jQuery.buildFragment( args, this[ 0 ].ownerDocument, false, this );
+			first = fragment.firstChild;
+
+			if ( fragment.childNodes.length === 1 ) {
+				fragment = first;
+			}
+
+			if ( first ) {
+				scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
+				hasScripts = scripts.length;
+
+				// Use the original fragment for the last item instead of the first because it can end up
+				// being emptied incorrectly in certain situations (#8070).
+				for ( ; i < l; i++ ) {
+					node = fragment;
+
+					if ( i !== iNoClone ) {
+						node = jQuery.clone( node, true, true );
+
+						// Keep references to cloned scripts for later restoration
+						if ( hasScripts ) {
+							jQuery.merge( scripts, getAll( node, "script" ) );
+						}
+					}
+
+					callback.call( this[i], node, i );
+				}
+
+				if ( hasScripts ) {
+					doc = scripts[ scripts.length - 1 ].ownerDocument;
+
+					// Reenable scripts
+					jQuery.map( scripts, restoreScript );
+
+					// Evaluate executable scripts on first document insertion
+					for ( i = 0; i < hasScripts; i++ ) {
+						node = scripts[ i ];
+						if ( rscriptType.test( node.type || "" ) &&
+							!jQuery._data( node, "globalEval" ) && jQuery.contains( doc, node ) ) {
+
+							if ( node.src ) {
+								// Optional AJAX dependency, but won't run scripts if not present
+								if ( jQuery._evalUrl ) {
+									jQuery._evalUrl( node.src );
+								}
+							} else {
+								jQuery.globalEval( ( node.text || node.textContent || node.innerHTML || "" ).replace( rcleanScript, "" ) );
+							}
+						}
+					}
+				}
+
+				// Fix #11809: Avoid leaking memory
+				fragment = first = null;
+			}
+		}
+
+		return this;
+	}
+});
+
+jQuery.each({
+	appendTo: "append",
+	prependTo: "prepend",
+	insertBefore: "before",
+	insertAfter: "after",
+	replaceAll: "replaceWith"
+}, function( name, original ) {
+	jQuery.fn[ name ] = function( selector ) {
+		var elems,
+			i = 0,
+			ret = [],
+			insert = jQuery( selector ),
+			last = insert.length - 1;
+
+		for ( ; i <= last; i++ ) {
+			elems = i === last ? this : this.clone(true);
+			jQuery( insert[i] )[ original ]( elems );
+
+			// Modern browsers can apply jQuery collections as arrays, but oldIE needs a .get()
+			push.apply( ret, elems.get() );
+		}
+
+		return this.pushStack( ret );
+	};
+});
+
+
+var iframe,
+	elemdisplay = {};
+
+/**
+ * Retrieve the actual display of a element
+ * @param {String} name nodeName of the element
+ * @param {Object} doc Document object
+ */
+// Called only from within defaultDisplay
+function actualDisplay( name, doc ) {
+	var style,
+		elem = jQuery( doc.createElement( name ) ).appendTo( doc.body ),
+
+		// getDefaultComputedStyle might be reliably used only on attached element
+		display = window.getDefaultComputedStyle && ( style = window.getDefaultComputedStyle( elem[ 0 ] ) ) ?
+
+			// Use of this method is a temporary fix (more like optmization) until something better comes along,
+			// since it was removed from specification and supported only in FF
+			style.display : jQuery.css( elem[ 0 ], "display" );
+
+	// We don't have any data stored on the element,
+	// so use "detach" method as fast way to get rid of the element
+	elem.detach();
+
+	return display;
+}
+
+/**
+ * Try to determine the default display value of an element
+ * @param {String} nodeName
+ */
+function defaultDisplay( nodeName ) {
+	var doc = document,
+		display = elemdisplay[ nodeName ];
+
+	if ( !display ) {
+		display = actualDisplay( nodeName, doc );
+
+		// If the simple way fails, read from inside an iframe
+		if ( display === "none" || !display ) {
+
+			// Use the already-created iframe if possible
+			iframe = (iframe || jQuery( "<iframe frameborder='0' width='0' height='0'/>" )).appendTo( doc.documentElement );
+
+			// Always write a new HTML skeleton so Webkit and Firefox don't choke on reuse
+			doc = ( iframe[ 0 ].contentWindow || iframe[ 0 ].contentDocument ).document;
+
+			// Support: IE
+			doc.write();
+			doc.close();
+
+			display = actualDisplay( nodeName, doc );
+			iframe.detach();
+		}
+
+		// Store the correct default display
+		elemdisplay[ nodeName ] = display;
+	}
+
+	return display;
+}
+
+
+(function() {
+	var shrinkWrapBlocksVal;
+
+	support.shrinkWrapBlocks = function() {
+		if ( shrinkWrapBlocksVal != null ) {
+			return shrinkWrapBlocksVal;
+		}
+
+		// Will be changed later if needed.
+		shrinkWrapBlocksVal = false;
+
+		// Minified: var b,c,d
+		var div, body, container;
+
+		body = document.getElementsByTagName( "body" )[ 0 ];
+		if ( !body || !body.style ) {
+			// Test fired too early or in an unsupported environment, exit.
+			return;
+		}
+
+		// Setup
+		div = document.createElement( "div" );
+		container = document.createElement( "div" );
+		container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
+		body.appendChild( container ).appendChild( div );
+
+		// Support: IE6
+		// Check if elements with layout shrink-wrap their children
+		if ( typeof div.style.zoom !== strundefined ) {
+			// Reset CSS: box-sizing; display; margin; border
+			div.style.cssText =
+				// Support: Firefox<29, Android 2.3
+				// Vendor-prefix box-sizing
+				"-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" +
+				"box-sizing:content-box;display:block;margin:0;border:0;" +
+				"padding:1px;width:1px;zoom:1";
+			div.appendChild( document.createElement( "div" ) ).style.width = "5px";
+			shrinkWrapBlocksVal = div.offsetWidth !== 3;
+		}
+
+		body.removeChild( container );
+
+		return shrinkWrapBlocksVal;
+	};
+
+})();
+var rmargin = (/^margin/);
+
+var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" );
+
+
+
+var getStyles, curCSS,
+	rposition = /^(top|right|bottom|left)$/;
+
+if ( window.getComputedStyle ) {
+	getStyles = function( elem ) {
+		return elem.ownerDocument.defaultView.getComputedStyle( elem, null );
+	};
+
+	curCSS = function( elem, name, computed ) {
+		var width, minWidth, maxWidth, ret,
+			style = elem.style;
+
+		computed = computed || getStyles( elem );
+
+		// getPropertyValue is only needed for .css('filter') in IE9, see #12537
+		ret = computed ? computed.getPropertyValue( name ) || computed[ name ] : undefined;
+
+		if ( computed ) {
+
+			if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) {
+				ret = jQuery.style( elem, name );
+			}
+
+			// A tribute to the "awesome hack by Dean Edwards"
+			// Chrome < 17 and Safari 5.0 uses "computed value" instead of "used value" for margin-right
+			// Safari 5.1.7 (at least) returns percentage for a larger set of values, but width seems to be reliably pixels
+			// this is against the CSSOM draft spec: http://dev.w3.org/csswg/cssom/#resolved-values
+			if ( rnumnonpx.test( ret ) && rmargin.test( name ) ) {
+
+				// Remember the original values
+				width = style.width;
+				minWidth = style.minWidth;
+				maxWidth = style.maxWidth;
+
+				// Put in the new values to get a computed value out
+				style.minWidth = style.maxWidth = style.width = ret;
+				ret = computed.width;
+
+				// Revert the changed values
+				style.width = width;
+				style.minWidth = minWidth;
+				style.maxWidth = maxWidth;
+			}
+		}
+
+		// Support: IE
+		// IE returns zIndex value as an integer.
+		return ret === undefined ?
+			ret :
+			ret + "";
+	};
+} else if ( document.documentElement.currentStyle ) {
+	getStyles = function( elem ) {
+		return elem.currentStyle;
+	};
+
+	curCSS = function( elem, name, computed ) {
+		var left, rs, rsLeft, ret,
+			style = elem.style;
+
+		computed = computed || getStyles( elem );
+		ret = computed ? computed[ name ] : undefined;
+
+		// Avoid setting ret to empty string here
+		// so we don't default to auto
+		if ( ret == null && style && style[ name ] ) {
+			ret = style[ name ];
+		}
+
+		// From the awesome hack by Dean Edwards
+		// http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291
+
+		// If we're not dealing with a regular pixel number
+		// but a number that has a weird ending, we need to convert it to pixels
+		// but not position css attributes, as those are proportional to the parent element instead
+		// and we can't measure the parent instead because it might trigger a "stacking dolls" problem
+		if ( rnumnonpx.test( ret ) && !rposition.test( name ) ) {
+
+			// Remember the original values
+			left = style.left;
+			rs = elem.runtimeStyle;
+			rsLeft = rs && rs.left;
+
+			// Put in the new values to get a computed value out
+			if ( rsLeft ) {
+				rs.left = elem.currentStyle.left;
+			}
+			style.left = name === "fontSize" ? "1em" : ret;
+			ret = style.pixelLeft + "px";
+
+			// Revert the changed values
+			style.left = left;
+			if ( rsLeft ) {
+				rs.left = rsLeft;
+			}
+		}
+
+		// Support: IE
+		// IE returns zIndex value as an integer.
+		return ret === undefined ?
+			ret :
+			ret + "" || "auto";
+	};
+}
+
+
+
+
+function addGetHookIf( conditionFn, hookFn ) {
+	// Define the hook, we'll check on the first run if it's really needed.
+	return {
+		get: function() {
+			var condition = conditionFn();
+
+			if ( condition == null ) {
+				// The test was not ready at this point; screw the hook this time
+				// but check again when needed next time.
+				return;
+			}
+
+			if ( condition ) {
+				// Hook not needed (or it's not possible to use it due to missing dependency),
+				// remove it.
+				// Since there are no other hooks for marginRight, remove the whole object.
+				delete this.get;
+				return;
+			}
+
+			// Hook needed; redefine it so that the support test is not executed again.
+
+			return (this.get = hookFn).apply( this, arguments );
+		}
+	};
+}
+
+
+(function() {
+	// Minified: var b,c,d,e,f,g, h,i
+	var div, style, a, pixelPositionVal, boxSizingReliableVal,
+		reliableHiddenOffsetsVal, reliableMarginRightVal;
+
+	// Setup
+	div = document.createElement( "div" );
+	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
+	a = div.getElementsByTagName( "a" )[ 0 ];
+	style = a && a.style;
+
+	// Finish early in limited (non-browser) environments
+	if ( !style ) {
+		return;
+	}
+
+	style.cssText = "float:left;opacity:.5";
+
+	// Support: IE<9
+	// Make sure that element opacity exists (as opposed to filter)
+	support.opacity = style.opacity === "0.5";
+
+	// Verify style float existence
+	// (IE uses styleFloat instead of cssFloat)
+	support.cssFloat = !!style.cssFloat;
+
+	div.style.backgroundClip = "content-box";
+	div.cloneNode( true ).style.backgroundClip = "";
+	support.clearCloneStyle = div.style.backgroundClip === "content-box";
+
+	// Support: Firefox<29, Android 2.3
+	// Vendor-prefix box-sizing
+	support.boxSizing = style.boxSizing === "" || style.MozBoxSizing === "" ||
+		style.WebkitBoxSizing === "";
+
+	jQuery.extend(support, {
+		reliableHiddenOffsets: function() {
+			if ( reliableHiddenOffsetsVal == null ) {
+				computeStyleTests();
+			}
+			return reliableHiddenOffsetsVal;
+		},
+
+		boxSizingReliable: function() {
+			if ( boxSizingReliableVal == null ) {
+				computeStyleTests();
+			}
+			return boxSizingReliableVal;
+		},
+
+		pixelPosition: function() {
+			if ( pixelPositionVal == null ) {
+				computeStyleTests();
+			}
+			return pixelPositionVal;
+		},
+
+		// Support: Android 2.3
+		reliableMarginRight: function() {
+			if ( reliableMarginRightVal == null ) {
+				computeStyleTests();
+			}
+			return reliableMarginRightVal;
+		}
+	});
+
+	function computeStyleTests() {
+		// Minified: var b,c,d,j
+		var div, body, container, contents;
+
+		body = document.getElementsByTagName( "body" )[ 0 ];
+		if ( !body || !body.style ) {
+			// Test fired too early or in an unsupported environment, exit.
+			return;
+		}
+
+		// Setup
+		div = document.createElement( "div" );
+		container = document.createElement( "div" );
+		container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
+		body.appendChild( container ).appendChild( div );
+
+		div.style.cssText =
+			// Support: Firefox<29, Android 2.3
+			// Vendor-prefix box-sizing
+			"-webkit-box-sizing:border-box;-moz-box-sizing:border-box;" +
+			"box-sizing:border-box;display:block;margin-top:1%;top:1%;" +
+			"border:1px;padding:1px;width:4px;position:absolute";
+
+		// Support: IE<9
+		// Assume reasonable values in the absence of getComputedStyle
+		pixelPositionVal = boxSizingReliableVal = false;
+		reliableMarginRightVal = true;
+
+		// Check for getComputedStyle so that this code is not run in IE<9.
+		if ( window.getComputedStyle ) {
+			pixelPositionVal = ( window.getComputedStyle( div, null ) || {} ).top !== "1%";
+			boxSizingReliableVal =
+				( window.getComputedStyle( div, null ) || { width: "4px" } ).width === "4px";
+
+			// Support: Android 2.3
+			// Div with explicit width and no margin-right incorrectly
+			// gets computed margin-right based on width of container (#3333)
+			// WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
+			contents = div.appendChild( document.createElement( "div" ) );
+
+			// Reset CSS: box-sizing; display; margin; border; padding
+			contents.style.cssText = div.style.cssText =
+				// Support: Firefox<29, Android 2.3
+				// Vendor-prefix box-sizing
+				"-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" +
+				"box-sizing:content-box;display:block;margin:0;border:0;padding:0";
+			contents.style.marginRight = contents.style.width = "0";
+			div.style.width = "1px";
+
+			reliableMarginRightVal =
+				!parseFloat( ( window.getComputedStyle( contents, null ) || {} ).marginRight );
+		}
+
+		// Support: IE8
+		// Check if table cells still have offsetWidth/Height when they are set
+		// to display:none and there are still other visible table cells in a
+		// table row; if so, offsetWidth/Height are not reliable for use when
+		// determining if an element has been hidden directly using
+		// display:none (it is still safe to use offsets if a parent element is
+		// hidden; don safety goggles and see bug #4512 for more information).
+		div.innerHTML = "<table><tr><td></td><td>t</td></tr></table>";
+		contents = div.getElementsByTagName( "td" );
+		contents[ 0 ].style.cssText = "margin:0;border:0;padding:0;display:none";
+		reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0;
+		if ( reliableHiddenOffsetsVal ) {
+			contents[ 0 ].style.display = "";
+			contents[ 1 ].style.display = "none";
+			reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0;
+		}
+
+		body.removeChild( container );
+	}
+
+})();
+
+
+// A method for quickly swapping in/out CSS properties to get correct calculations.
+jQuery.swap = function( elem, options, callback, args ) {
+	var ret, name,
+		old = {};
+
+	// Remember the old values, and insert the new ones
+	for ( name in options ) {
+		old[ name ] = elem.style[ name ];
+		elem.style[ name ] = options[ name ];
+	}
+
+	ret = callback.apply( elem, args || [] );
+
+	// Revert the old values
+	for ( name in options ) {
+		elem.style[ name ] = old[ name ];
+	}
+
+	return ret;
+};
+
+
+var
+		ralpha = /alpha\([^)]*\)/i,
+	ropacity = /opacity\s*=\s*([^)]*)/,
+
+	// swappable if display is none or starts with table except "table", "table-cell", or "table-caption"
+	// see here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
+	rdisplayswap = /^(none|table(?!-c[ea]).+)/,
+	rnumsplit = new RegExp( "^(" + pnum + ")(.*)$", "i" ),
+	rrelNum = new RegExp( "^([+-])=(" + pnum + ")", "i" ),
+
+	cssShow = { position: "absolute", visibility: "hidden", display: "block" },
+	cssNormalTransform = {
+		letterSpacing: "0",
+		fontWeight: "400"
+	},
+
+	cssPrefixes = [ "Webkit", "O", "Moz", "ms" ];
+
+
+// return a css property mapped to a potentially vendor prefixed property
+function vendorPropName( style, name ) {
+
+	// shortcut for names that are not vendor prefixed
+	if ( name in style ) {
+		return name;
+	}
+
+	// check for vendor prefixed names
+	var capName = name.charAt(0).toUpperCase() + name.slice(1),
+		origName = name,
+		i = cssPrefixes.length;
+
+	while ( i-- ) {
+		name = cssPrefixes[ i ] + capName;
+		if ( name in style ) {
+			return name;
+		}
+	}
+
+	return origName;
+}
+
+function showHide( elements, show ) {
+	var display, elem, hidden,
+		values = [],
+		index = 0,
+		length = elements.length;
+
+	for ( ; index < length; index++ ) {
+		elem = elements[ index ];
+		if ( !elem.style ) {
+			continue;
+		}
+
+		values[ index ] = jQuery._data( elem, "olddisplay" );
+		display = elem.style.display;
+		if ( show ) {
+			// Reset the inline display of this element to learn if it is
+			// being hidden by cascaded rules or not
+			if ( !values[ index ] && display === "none" ) {
+				elem.style.display = "";
+			}
+
+			// Set elements which have been overridden with display: none
+			// in a stylesheet to whatever the default browser style is
+			// for such an element
+			if ( elem.style.display === "" && isHidden( elem ) ) {
+				values[ index ] = jQuery._data( elem, "olddisplay", defaultDisplay(elem.nodeName) );
+			}
+		} else {
+			hidden = isHidden( elem );
+
+			if ( display && display !== "none" || !hidden ) {
+				jQuery._data( elem, "olddisplay", hidden ? display : jQuery.css( elem, "display" ) );
+			}
+		}
+	}
+
+	// Set the display of most of the elements in a second loop
+	// to avoid the constant reflow
+	for ( index = 0; index < length; index++ ) {
+		elem = elements[ index ];
+		if ( !elem.style ) {
+			continue;
+		}
+		if ( !show || elem.style.display === "none" || elem.style.display === "" ) {
+			elem.style.display = show ? values[ index ] || "" : "none";
+		}
+	}
+
+	return elements;
+}
+
+function setPositiveNumber( elem, value, subtract ) {
+	var matches = rnumsplit.exec( value );
+	return matches ?
+		// Guard against undefined "subtract", e.g., when used as in cssHooks
+		Math.max( 0, matches[ 1 ] - ( subtract || 0 ) ) + ( matches[ 2 ] || "px" ) :
+		value;
+}
+
+function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) {
+	var i = extra === ( isBorderBox ? "border" : "content" ) ?
+		// If we already have the right measurement, avoid augmentation
+		4 :
+		// Otherwise initialize for horizontal or vertical properties
+		name === "width" ? 1 : 0,
+
+		val = 0;
+
+	for ( ; i < 4; i += 2 ) {
+		// both box models exclude margin, so add it if we want it
+		if ( extra === "margin" ) {
+			val += jQuery.css( elem, extra + cssExpand[ i ], true, styles );
+		}
+
+		if ( isBorderBox ) {
+			// border-box includes padding, so remove it if we want content
+			if ( extra === "content" ) {
+				val -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
+			}
+
+			// at this point, extra isn't border nor margin, so remove border
+			if ( extra !== "margin" ) {
+				val -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+			}
+		} else {
+			// at this point, extra isn't content, so add padding
+			val += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
+
+			// at this point, extra isn't content nor padding, so add border
+			if ( extra !== "padding" ) {
+				val += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+			}
+		}
+	}
+
+	return val;
+}
+
+function getWidthOrHeight( elem, name, extra ) {
+
+	// Start with offset property, which is equivalent to the border-box value
+	var valueIsBorderBox = true,
+		val = name === "width" ? elem.offsetWidth : elem.offsetHeight,
+		styles = getStyles( elem ),
+		isBorderBox = support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
+
+	// some non-html elements return undefined for offsetWidth, so check for null/undefined
+	// svg - https://bugzilla.mozilla.org/show_bug.cgi?id=649285
+	// MathML - https://bugzilla.mozilla.org/show_bug.cgi?id=491668
+	if ( val <= 0 || val == null ) {
+		// Fall back to computed then uncomputed css if necessary
+		val = curCSS( elem, name, styles );
+		if ( val < 0 || val == null ) {
+			val = elem.style[ name ];
+		}
+
+		// Computed unit is not pixels. Stop here and return.
+		if ( rnumnonpx.test(val) ) {
+			return val;
+		}
+
+		// we need the check for style in case a browser which returns unreliable values
+		// for getComputedStyle silently falls back to the reliable elem.style
+		valueIsBorderBox = isBorderBox && ( support.boxSizingReliable() || val === elem.style[ name ] );
+
+		// Normalize "", auto, and prepare for extra
+		val = parseFloat( val ) || 0;
+	}
+
+	// use the active box-sizing model to add/subtract irrelevant styles
+	return ( val +
+		augmentWidthOrHeight(
+			elem,
+			name,
+			extra || ( isBorderBox ? "border" : "content" ),
+			valueIsBorderBox,
+			styles
+		)
+	) + "px";
+}
+
+jQuery.extend({
+	// Add in style property hooks for overriding the default
+	// behavior of getting and setting a style property
+	cssHooks: {
+		opacity: {
+			get: function( elem, computed ) {
+				if ( computed ) {
+					// We should always get a number back from opacity
+					var ret = curCSS( elem, "opacity" );
+					return ret === "" ? "1" : ret;
+				}
+			}
+		}
+	},
+
+	// Don't automatically add "px" to these possibly-unitless properties
+	cssNumber: {
+		"columnCount": true,
+		"fillOpacity": true,
+		"flexGrow": true,
+		"flexShrink": true,
+		"fontWeight": true,
+		"lineHeight": true,
+		"opacity": true,
+		"order": true,
+		"orphans": true,
+		"widows": true,
+		"zIndex": true,
+		"zoom": true
+	},
+
+	// Add in properties whose names you wish to fix before
+	// setting or getting the value
+	cssProps: {
+		// normalize float css property
+		"float": support.cssFloat ? "cssFloat" : "styleFloat"
+	},
+
+	// Get and set the style property on a DOM Node
+	style: function( elem, name, value, extra ) {
+		// Don't set styles on text and comment nodes
+		if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
+			return;
+		}
+
+		// Make sure that we're working with the right name
+		var ret, type, hooks,
+			origName = jQuery.camelCase( name ),
+			style = elem.style;
+
+		name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( style, origName ) );
+
+		// gets hook for the prefixed version
+		// followed by the unprefixed version
+		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+		// Check if we're setting a value
+		if ( value !== undefined ) {
+			type = typeof value;
+
+			// convert relative number strings (+= or -=) to relative numbers. #7345
+			if ( type === "string" && (ret = rrelNum.exec( value )) ) {
+				value = ( ret[1] + 1 ) * ret[2] + parseFloat( jQuery.css( elem, name ) );
+				// Fixes bug #9237
+				type = "number";
+			}
+
+			// Make sure that null and NaN values aren't set. See: #7116
+			if ( value == null || value !== value ) {
+				return;
+			}
+
+			// If a number was passed in, add 'px' to the (except for certain CSS properties)
+			if ( type === "number" && !jQuery.cssNumber[ origName ] ) {
+				value += "px";
+			}
+
+			// Fixes #8908, it can be done more correctly by specifing setters in cssHooks,
+			// but it would mean to define eight (for every problematic property) identical functions
+			if ( !support.clearCloneStyle && value === "" && name.indexOf("background") === 0 ) {
+				style[ name ] = "inherit";
+			}
+
+			// If a hook was provided, use that value, otherwise just set the specified value
+			if ( !hooks || !("set" in hooks) || (value = hooks.set( elem, value, extra )) !== undefined ) {
+
+				// Support: IE
+				// Swallow errors from 'invalid' CSS values (#5509)
+				try {
+					style[ name ] = value;
+				} catch(e) {}
+			}
+
+		} else {
+			// If a hook was provided get the non-computed value from there
+			if ( hooks && "get" in hooks && (ret = hooks.get( elem, false, extra )) !== undefined ) {
+				return ret;
+			}
+
+			// Otherwise just get the value from the style object
+			return style[ name ];
+		}
+	},
+
+	css: function( elem, name, extra, styles ) {
+		var num, val, hooks,
+			origName = jQuery.camelCase( name );
+
+		// Make sure that we're working with the right name
+		name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( elem.style, origName ) );
+
+		// gets hook for the prefixed version
+		// followed by the unprefixed version
+		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+		// If a hook was provided get the computed value from there
+		if ( hooks && "get" in hooks ) {
+			val = hooks.get( elem, true, extra );
+		}
+
+		// Otherwise, if a way to get the computed value exists, use that
+		if ( val === undefined ) {
+			val = curCSS( elem, name, styles );
+		}
+
+		//convert "normal" to computed value
+		if ( val === "normal" && name in cssNormalTransform ) {
+			val = cssNormalTransform[ name ];
+		}
+
+		// Return, converting to number if forced or a qualifier was provided and val looks numeric
+		if ( extra === "" || extra ) {
+			num = parseFloat( val );
+			return extra === true || jQuery.isNumeric( num ) ? num || 0 : val;
+		}
+		return val;
+	}
+});
+
+jQuery.each([ "height", "width" ], function( i, name ) {
+	jQuery.cssHooks[ name ] = {
+		get: function( elem, computed, extra ) {
+			if ( computed ) {
+				// certain elements can have dimension info if we invisibly show them
+				// however, it must have a current display style that would benefit from this
+				return rdisplayswap.test( jQuery.css( elem, "display" ) ) && elem.offsetWidth === 0 ?
+					jQuery.swap( elem, cssShow, function() {
+						return getWidthOrHeight( elem, name, extra );
+					}) :
+					getWidthOrHeight( elem, name, extra );
+			}
+		},
+
+		set: function( elem, value, extra ) {
+			var styles = extra && getStyles( elem );
+			return setPositiveNumber( elem, value, extra ?
+				augmentWidthOrHeight(
+					elem,
+					name,
+					extra,
+					support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
+					styles
+				) : 0
+			);
+		}
+	};
+});
+
+if ( !support.opacity ) {
+	jQuery.cssHooks.opacity = {
+		get: function( elem, computed ) {
+			// IE uses filters for opacity
+			return ropacity.test( (computed && elem.currentStyle ? elem.currentStyle.filter : elem.style.filter) || "" ) ?
+				( 0.01 * parseFloat( RegExp.$1 ) ) + "" :
+				computed ? "1" : "";
+		},
+
+		set: function( elem, value ) {
+			var style = elem.style,
+				currentStyle = elem.currentStyle,
+				opacity = jQuery.isNumeric( value ) ? "alpha(opacity=" + value * 100 + ")" : "",
+				filter = currentStyle && currentStyle.filter || style.filter || "";
+
+			// IE has trouble with opacity if it does not have layout
+			// Force it by setting the zoom level
+			style.zoom = 1;
+
+			// if setting opacity to 1, and no other filters exist - attempt to remove filter attribute #6652
+			// if value === "", then remove inline opacity #12685
+			if ( ( value >= 1 || value === "" ) &&
+					jQuery.trim( filter.replace( ralpha, "" ) ) === "" &&
+					style.removeAttribute ) {
+
+				// Setting style.filter to null, "" & " " still leave "filter:" in the cssText
+				// if "filter:" is present at all, clearType is disabled, we want to avoid this
+				// style.removeAttribute is IE Only, but so apparently is this code path...
+				style.removeAttribute( "filter" );
+
+				// if there is no filter style applied in a css rule or unset inline opacity, we are done
+				if ( value === "" || currentStyle && !currentStyle.filter ) {
+					return;
+				}
+			}
+
+			// otherwise, set new filter values
+			style.filter = ralpha.test( filter ) ?
+				filter.replace( ralpha, opacity ) :
+				filter + " " + opacity;
+		}
+	};
+}
+
+jQuery.cssHooks.marginRight = addGetHookIf( support.reliableMarginRight,
+	function( elem, computed ) {
+		if ( computed ) {
+			// WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
+			// Work around by temporarily setting element display to inline-block
+			return jQuery.swap( elem, { "display": "inline-block" },
+				curCSS, [ elem, "marginRight" ] );
+		}
+	}
+);
+
+// These hooks are used by animate to expand properties
+jQuery.each({
+	margin: "",
+	padding: "",
+	border: "Width"
+}, function( prefix, suffix ) {
+	jQuery.cssHooks[ prefix + suffix ] = {
+		expand: function( value ) {
+			var i = 0,
+				expanded = {},
+
+				// assumes a single number if not a string
+				parts = typeof value === "string" ? value.split(" ") : [ value ];
+
+			for ( ; i < 4; i++ ) {
+				expanded[ prefix + cssExpand[ i ] + suffix ] =
+					parts[ i ] || parts[ i - 2 ] || parts[ 0 ];
+			}
+
+			return expanded;
+		}
+	};
+
+	if ( !rmargin.test( prefix ) ) {
+		jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber;
+	}
+});
+
+jQuery.fn.extend({
+	css: function( name, value ) {
+		return access( this, function( elem, name, value ) {
+			var styles, len,
+				map = {},
+				i = 0;
+
+			if ( jQuery.isArray( name ) ) {
+				styles = getStyles( elem );
+				len = name.length;
+
+				for ( ; i < len; i++ ) {
+					map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles );
+				}
+
+				return map;
+			}
+
+			return value !== undefined ?
+				jQuery.style( elem, name, value ) :
+				jQuery.css( elem, name );
+		}, name, value, arguments.length > 1 );
+	},
+	show: function() {
+		return showHide( this, true );
+	},
+	hide: function() {
+		return showHide( this );
+	},
+	toggle: function( state ) {
+		if ( typeof state === "boolean" ) {
+			return state ? this.show() : this.hide();
+		}
+
+		return this.each(function() {
+			if ( isHidden( this ) ) {
+				jQuery( this ).show();
+			} else {
+				jQuery( this ).hide();
+			}
+		});
+	}
+});
+
+
+function Tween( elem, options, prop, end, easing ) {
+	return new Tween.prototype.init( elem, options, prop, end, easing );
+}
+jQuery.Tween = Tween;
+
+Tween.prototype = {
+	constructor: Tween,
+	init: function( elem, options, prop, end, easing, unit ) {
+		this.elem = elem;
+		this.prop = prop;
+		this.easing = easing || "swing";
+		this.options = options;
+		this.start = this.now = this.cur();
+		this.end = end;
+		this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" );
+	},
+	cur: function() {
+		var hooks = Tween.propHooks[ this.prop ];
+
+		return hooks && hooks.get ?
+			hooks.get( this ) :
+			Tween.propHooks._default.get( this );
+	},
+	run: function( percent ) {
+		var eased,
+			hooks = Tween.propHooks[ this.prop ];
+
+		if ( this.options.duration ) {
+			this.pos = eased = jQuery.easing[ this.easing ](
+				percent, this.options.duration * percent, 0, 1, this.options.duration
+			);
+		} else {
+			this.pos = eased = percent;
+		}
+		this.now = ( this.end - this.start ) * eased + this.start;
+
+		if ( this.options.step ) {
+			this.options.step.call( this.elem, this.now, this );
+		}
+
+		if ( hooks && hooks.set ) {
+			hooks.set( this );
+		} else {
+			Tween.propHooks._default.set( this );
+		}
+		return this;
+	}
+};
+
+Tween.prototype.init.prototype = Tween.prototype;
+
+Tween.propHooks = {
+	_default: {
+		get: function( tween ) {
+			var result;
+
+			if ( tween.elem[ tween.prop ] != null &&
+				(!tween.elem.style || tween.elem.style[ tween.prop ] == null) ) {
+				return tween.elem[ tween.prop ];
+			}
+
+			// passing an empty string as a 3rd parameter to .css will automatically
+			// attempt a parseFloat and fallback to a string if the parse fails
+			// so, simple values such as "10px" are parsed to Float.
+			// complex values such as "rotate(1rad)" are returned as is.
+			result = jQuery.css( tween.elem, tween.prop, "" );
+			// Empty strings, null, undefined and "auto" are converted to 0.
+			return !result || result === "auto" ? 0 : result;
+		},
+		set: function( tween ) {
+			// use step hook for back compat - use cssHook if its there - use .style if its
+			// available and use plain properties where available
+			if ( jQuery.fx.step[ tween.prop ] ) {
+				jQuery.fx.step[ tween.prop ]( tween );
+			} else if ( tween.elem.style && ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null || jQuery.cssHooks[ tween.prop ] ) ) {
+				jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
+			} else {
+				tween.elem[ tween.prop ] = tween.now;
+			}
+		}
+	}
+};
+
+// Support: IE <=9
+// Panic based approach to setting things on disconnected nodes
+
+Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
+	set: function( tween ) {
+		if ( tween.elem.nodeType && tween.elem.parentNode ) {
+			tween.elem[ tween.prop ] = tween.now;
+		}
+	}
+};
+
+jQuery.easing = {
+	linear: function( p ) {
+		return p;
+	},
+	swing: function( p ) {
+		return 0.5 - Math.cos( p * Math.PI ) / 2;
+	}
+};
+
+jQuery.fx = Tween.prototype.init;
+
+// Back Compat <1.8 extension point
+jQuery.fx.step = {};
+
+
+
+
+var
+	fxNow, timerId,
+	rfxtypes = /^(?:toggle|show|hide)$/,
+	rfxnum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ),
+	rrun = /queueHooks$/,
+	animationPrefilters = [ defaultPrefilter ],
+	tweeners = {
+		"*": [ function( prop, value ) {
+			var tween = this.createTween( prop, value ),
+				target = tween.cur(),
+				parts = rfxnum.exec( value ),
+				unit = parts && parts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ),
+
+				// Starting value computation is required for potential unit mismatches
+				start = ( jQuery.cssNumber[ prop ] || unit !== "px" && +target ) &&
+					rfxnum.exec( jQuery.css( tween.elem, prop ) ),
+				scale = 1,
+				maxIterations = 20;
+
+			if ( start && start[ 3 ] !== unit ) {
+				// Trust units reported by jQuery.css
+				unit = unit || start[ 3 ];
+
+				// Make sure we update the tween properties later on
+				parts = parts || [];
+
+				// Iteratively approximate from a nonzero starting point
+				start = +target || 1;
+
+				do {
+					// If previous iteration zeroed out, double until we get *something*
+					// Use a string for doubling factor so we don't accidentally see scale as unchanged below
+					scale = scale || ".5";
+
+					// Adjust and apply
+					start = start / scale;
+					jQuery.style( tween.elem, prop, start + unit );
+
+				// Update scale, tolerating zero or NaN from tween.cur()
+				// And breaking the loop if scale is unchanged or perfect, or if we've just had enough
+				} while ( scale !== (scale = tween.cur() / target) && scale !== 1 && --maxIterations );
+			}
+
+			// Update tween properties
+			if ( parts ) {
+				start = tween.start = +start || +target || 0;
+				tween.unit = unit;
+				// If a +=/-= token was provided, we're doing a relative animation
+				tween.end = parts[ 1 ] ?
+					start + ( parts[ 1 ] + 1 ) * parts[ 2 ] :
+					+parts[ 2 ];
+			}
+
+			return tween;
+		} ]
+	};
+
+// Animations created synchronously will run synchronously
+function createFxNow() {
+	setTimeout(function() {
+		fxNow = undefined;
+	});
+	return ( fxNow = jQuery.now() );
+}
+
+// Generate parameters to create a standard animation
+function genFx( type, includeWidth ) {
+	var which,
+		attrs = { height: type },
+		i = 0;
+
+	// if we include width, step value is 1 to do all cssExpand values,
+	// if we don't include width, step value is 2 to skip over Left and Right
+	includeWidth = includeWidth ? 1 : 0;
+	for ( ; i < 4 ; i += 2 - includeWidth ) {
+		which = cssExpand[ i ];
+		attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
+	}
+
+	if ( includeWidth ) {
+		attrs.opacity = attrs.width = type;
+	}
+
+	return attrs;
+}
+
+function createTween( value, prop, animation ) {
+	var tween,
+		collection = ( tweeners[ prop ] || [] ).concat( tweeners[ "*" ] ),
+		index = 0,
+		length = collection.length;
+	for ( ; index < length; index++ ) {
+		if ( (tween = collection[ index ].call( animation, prop, value )) ) {
+
+			// we're done with this property
+			return tween;
+		}
+	}
+}
+
+function defaultPrefilter( elem, props, opts ) {
+	/* jshint validthis: true */
+	var prop, value, toggle, tween, hooks, oldfire, display, checkDisplay,
+		anim = this,
+		orig = {},
+		style = elem.style,
+		hidden = elem.nodeType && isHidden( elem ),
+		dataShow = jQuery._data( elem, "fxshow" );
+
+	// handle queue: false promises
+	if ( !opts.queue ) {
+		hooks = jQuery._queueHooks( elem, "fx" );
+		if ( hooks.unqueued == null ) {
+			hooks.unqueued = 0;
+			oldfire = hooks.empty.fire;
+			hooks.empty.fire = function() {
+				if ( !hooks.unqueued ) {
+					oldfire();
+				}
+			};
+		}
+		hooks.unqueued++;
+
+		anim.always(function() {
+			// doing this makes sure that the complete handler will be called
+			// before this completes
+			anim.always(function() {
+				hooks.unqueued--;
+				if ( !jQuery.queue( elem, "fx" ).length ) {
+					hooks.empty.fire();
+				}
+			});
+		});
+	}
+
+	// height/width overflow pass
+	if ( elem.nodeType === 1 && ( "height" in props || "width" in props ) ) {
+		// Make sure that nothing sneaks out
+		// Record all 3 overflow attributes because IE does not
+		// change the overflow attribute when overflowX and
+		// overflowY are set to the same value
+		opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
+
+		// Set display property to inline-block for height/width
+		// animations on inline elements that are having width/height animated
+		display = jQuery.css( elem, "display" );
+
+		// Test default display if display is currently "none"
+		checkDisplay = display === "none" ?
+			jQuery._data( elem, "olddisplay" ) || defaultDisplay( elem.nodeName ) : display;
+
+		if ( checkDisplay === "inline" && jQuery.css( elem, "float" ) === "none" ) {
+
+			// inline-level elements accept inline-block;
+			// block-level elements need to be inline with layout
+			if ( !support.inlineBlockNeedsLayout || defaultDisplay( elem.nodeName ) === "inline" ) {
+				style.display = "inline-block";
+			} else {
+				style.zoom = 1;
+			}
+		}
+	}
+
+	if ( opts.overflow ) {
+		style.overflow = "hidden";
+		if ( !support.shrinkWrapBlocks() ) {
+			anim.always(function() {
+				style.overflow = opts.overflow[ 0 ];
+				style.overflowX = opts.overflow[ 1 ];
+				style.overflowY = opts.overflow[ 2 ];
+			});
+		}
+	}
+
+	// show/hide pass
+	for ( prop in props ) {
+		value = props[ prop ];
+		if ( rfxtypes.exec( value ) ) {
+			delete props[ prop ];
+			toggle = toggle || value === "toggle";
+			if ( value === ( hidden ? "hide" : "show" ) ) {
+
+				// If there is dataShow left over from a stopped hide or show and we are going to proceed with show, we should pretend to be hidden
+				if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) {
+					hidden = true;
+				} else {
+					continue;
+				}
+			}
+			orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop );
+
+		// Any non-fx value stops us from restoring the original display value
+		} else {
+			display = undefined;
+		}
+	}
+
+	if ( !jQuery.isEmptyObject( orig ) ) {
+		if ( dataShow ) {
+			if ( "hidden" in dataShow ) {
+				hidden = dataShow.hidden;
+			}
+		} else {
+			dataShow = jQuery._data( elem, "fxshow", {} );
+		}
+
+		// store state if its toggle - enables .stop().toggle() to "reverse"
+		if ( toggle ) {
+			dataShow.hidden = !hidden;
+		}
+		if ( hidden ) {
+			jQuery( elem ).show();
+		} else {
+			anim.done(function() {
+				jQuery( elem ).hide();
+			});
+		}
+		anim.done(function() {
+			var prop;
+			jQuery._removeData( elem, "fxshow" );
+			for ( prop in orig ) {
+				jQuery.style( elem, prop, orig[ prop ] );
+			}
+		});
+		for ( prop in orig ) {
+			tween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim );
+
+			if ( !( prop in dataShow ) ) {
+				dataShow[ prop ] = tween.start;
+				if ( hidden ) {
+					tween.end = tween.start;
+					tween.start = prop === "width" || prop === "height" ? 1 : 0;
+				}
+			}
+		}
+
+	// If this is a noop like .hide().hide(), restore an overwritten display value
+	} else if ( (display === "none" ? defaultDisplay( elem.nodeName ) : display) === "inline" ) {
+		style.display = display;
+	}
+}
+
+function propFilter( props, specialEasing ) {
+	var index, name, easing, value, hooks;
+
+	// camelCase, specialEasing and expand cssHook pass
+	for ( index in props ) {
+		name = jQuery.camelCase( index );
+		easing = specialEasing[ name ];
+		value = props[ index ];
+		if ( jQuery.isArray( value ) ) {
+			easing = value[ 1 ];
+			value = props[ index ] = value[ 0 ];
+		}
+
+		if ( index !== name ) {
+			props[ name ] = value;
+			delete props[ index ];
+		}
+
+		hooks = jQuery.cssHooks[ name ];
+		if ( hooks && "expand" in hooks ) {
+			value = hooks.expand( value );
+			delete props[ name ];
+
+			// not quite $.extend, this wont overwrite keys already present.
+			// also - reusing 'index' from above because we have the correct "name"
+			for ( index in value ) {
+				if ( !( index in props ) ) {
+					props[ index ] = value[ index ];
+					specialEasing[ index ] = easing;
+				}
+			}
+		} else {
+			specialEasing[ name ] = easing;
+		}
+	}
+}
+
+function Animation( elem, properties, options ) {
+	var result,
+		stopped,
+		index = 0,
+		length = animationPrefilters.length,
+		deferred = jQuery.Deferred().always( function() {
+			// don't match elem in the :animated selector
+			delete tick.elem;
+		}),
+		tick = function() {
+			if ( stopped ) {
+				return false;
+			}
+			var currentTime = fxNow || createFxNow(),
+				remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
+				// archaic crash bug won't allow us to use 1 - ( 0.5 || 0 ) (#12497)
+				temp = remaining / animation.duration || 0,
+				percent = 1 - temp,
+				index = 0,
+				length = animation.tweens.length;
+
+			for ( ; index < length ; index++ ) {
+				animation.tweens[ index ].run( percent );
+			}
+
+			deferred.notifyWith( elem, [ animation, percent, remaining ]);
+
+			if ( percent < 1 && length ) {
+				return remaining;
+			} else {
+				deferred.resolveWith( elem, [ animation ] );
+				return false;
+			}
+		},
+		animation = deferred.promise({
+			elem: elem,
+			props: jQuery.extend( {}, properties ),
+			opts: jQuery.extend( true, { specialEasing: {} }, options ),
+			originalProperties: properties,
+			originalOptions: options,
+			startTime: fxNow || createFxNow(),
+			duration: options.duration,
+			tweens: [],
+			createTween: function( prop, end ) {
+				var tween = jQuery.Tween( elem, animation.opts, prop, end,
+						animation.opts.specialEasing[ prop ] || animation.opts.easing );
+				animation.tweens.push( tween );
+				return tween;
+			},
+			stop: function( gotoEnd ) {
+				var index = 0,
+					// if we are going to the end, we want to run all the tweens
+					// otherwise we skip this part
+					length = gotoEnd ? animation.tweens.length : 0;
+				if ( stopped ) {
+					return this;
+				}
+				stopped = true;
+				for ( ; index < length ; index++ ) {
+					animation.tweens[ index ].run( 1 );
+				}
+
+				// resolve when we played the last frame
+				// otherwise, reject
+				if ( gotoEnd ) {
+					deferred.resolveWith( elem, [ animation, gotoEnd ] );
+				} else {
+					deferred.rejectWith( elem, [ animation, gotoEnd ] );
+				}
+				return this;
+			}
+		}),
+		props = animation.props;
+
+	propFilter( props, animation.opts.specialEasing );
+
+	for ( ; index < length ; index++ ) {
+		result = animationPrefilters[ index ].call( animation, elem, props, animation.opts );
+		if ( result ) {
+			return result;
+		}
+	}
+
+	jQuery.map( props, createTween, animation );
+
+	if ( jQuery.isFunction( animation.opts.start ) ) {
+		animation.opts.start.call( elem, animation );
+	}
+
+	jQuery.fx.timer(
+		jQuery.extend( tick, {
+			elem: elem,
+			anim: animation,
+			queue: animation.opts.queue
+		})
+	);
+
+	// attach callbacks from options
+	return animation.progress( animation.opts.progress )
+		.done( animation.opts.done, animation.opts.complete )
+		.fail( animation.opts.fail )
+		.always( animation.opts.always );
+}
+
+jQuery.Animation = jQuery.extend( Animation, {
+	tweener: function( props, callback ) {
+		if ( jQuery.isFunction( props ) ) {
+			callback = props;
+			props = [ "*" ];
+		} else {
+			props = props.split(" ");
+		}
+
+		var prop,
+			index = 0,
+			length = props.length;
+
+		for ( ; index < length ; index++ ) {
+			prop = props[ index ];
+			tweeners[ prop ] = tweeners[ prop ] || [];
+			tweeners[ prop ].unshift( callback );
+		}
+	},
+
+	prefilter: function( callback, prepend ) {
+		if ( prepend ) {
+			animationPrefilters.unshift( callback );
+		} else {
+			animationPrefilters.push( callback );
+		}
+	}
+});
+
+jQuery.speed = function( speed, easing, fn ) {
+	var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
+		complete: fn || !fn && easing ||
+			jQuery.isFunction( speed ) && speed,
+		duration: speed,
+		easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing
+	};
+
+	opt.duration = jQuery.fx.off ? 0 : typeof opt.duration === "number" ? opt.duration :
+		opt.duration in jQuery.fx.speeds ? jQuery.fx.speeds[ opt.duration ] : jQuery.fx.speeds._default;
+
+	// normalize opt.queue - true/undefined/null -> "fx"
+	if ( opt.queue == null || opt.queue === true ) {
+		opt.queue = "fx";
+	}
+
+	// Queueing
+	opt.old = opt.complete;
+
+	opt.complete = function() {
+		if ( jQuery.isFunction( opt.old ) ) {
+			opt.old.call( this );
+		}
+
+		if ( opt.queue ) {
+			jQuery.dequeue( this, opt.queue );
+		}
+	};
+
+	return opt;
+};
+
+jQuery.fn.extend({
+	fadeTo: function( speed, to, easing, callback ) {
+
+		// show any hidden elements after setting opacity to 0
+		return this.filter( isHidden ).css( "opacity", 0 ).show()
+
+			// animate to the value specified
+			.end().animate({ opacity: to }, speed, easing, callback );
+	},
+	animate: function( prop, speed, easing, callback ) {
+		var empty = jQuery.isEmptyObject( prop ),
+			optall = jQuery.speed( speed, easing, callback ),
+			doAnimation = function() {
+				// Operate on a copy of prop so per-property easing won't be lost
+				var anim = Animation( this, jQuery.extend( {}, prop ), optall );
+
+				// Empty animations, or finishing resolves immediately
+				if ( empty || jQuery._data( this, "finish" ) ) {
+					anim.stop( true );
+				}
+			};
+			doAnimation.finish = doAnimation;
+
+		return empty || optall.queue === false ?
+			this.each( doAnimation ) :
+			this.queue( optall.queue, doAnimation );
+	},
+	stop: function( type, clearQueue, gotoEnd ) {
+		var stopQueue = function( hooks ) {
+			var stop = hooks.stop;
+			delete hooks.stop;
+			stop( gotoEnd );
+		};
+
+		if ( typeof type !== "string" ) {
+			gotoEnd = clearQueue;
+			clearQueue = type;
+			type = undefined;
+		}
+		if ( clearQueue && type !== false ) {
+			this.queue( type || "fx", [] );
+		}
+
+		return this.each(function() {
+			var dequeue = true,
+				index = type != null && type + "queueHooks",
+				timers = jQuery.timers,
+				data = jQuery._data( this );
+
+			if ( index ) {
+				if ( data[ index ] && data[ index ].stop ) {
+					stopQueue( data[ index ] );
+				}
+			} else {
+				for ( index in data ) {
+					if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) {
+						stopQueue( data[ index ] );
+					}
+				}
+			}
+
+			for ( index = timers.length; index--; ) {
+				if ( timers[ index ].elem === this && (type == null || timers[ index ].queue === type) ) {
+					timers[ index ].anim.stop( gotoEnd );
+					dequeue = false;
+					timers.splice( index, 1 );
+				}
+			}
+
+			// start the next in the queue if the last step wasn't forced
+			// timers currently will call their complete callbacks, which will dequeue
+			// but only if they were gotoEnd
+			if ( dequeue || !gotoEnd ) {
+				jQuery.dequeue( this, type );
+			}
+		});
+	},
+	finish: function( type ) {
+		if ( type !== false ) {
+			type = type || "fx";
+		}
+		return this.each(function() {
+			var index,
+				data = jQuery._data( this ),
+				queue = data[ type + "queue" ],
+				hooks = data[ type + "queueHooks" ],
+				timers = jQuery.timers,
+				length = queue ? queue.length : 0;
+
+			// enable finishing flag on private data
+			data.finish = true;
+
+			// empty the queue first
+			jQuery.queue( this, type, [] );
+
+			if ( hooks && hooks.stop ) {
+				hooks.stop.call( this, true );
+			}
+
+			// look for any active animations, and finish them
+			for ( index = timers.length; index--; ) {
+				if ( timers[ index ].elem === this && timers[ index ].queue === type ) {
+					timers[ index ].anim.stop( true );
+					timers.splice( index, 1 );
+				}
+			}
+
+			// look for any animations in the old queue and finish them
+			for ( index = 0; index < length; index++ ) {
+				if ( queue[ index ] && queue[ index ].finish ) {
+					queue[ index ].finish.call( this );
+				}
+			}
+
+			// turn off finishing flag
+			delete data.finish;
+		});
+	}
+});
+
+jQuery.each([ "toggle", "show", "hide" ], function( i, name ) {
+	var cssFn = jQuery.fn[ name ];
+	jQuery.fn[ name ] = function( speed, easing, callback ) {
+		return speed == null || typeof speed === "boolean" ?
+			cssFn.apply( this, arguments ) :
+			this.animate( genFx( name, true ), speed, easing, callback );
+	};
+});
+
+// Generate shortcuts for custom animations
+jQuery.each({
+	slideDown: genFx("show"),
+	slideUp: genFx("hide"),
+	slideToggle: genFx("toggle"),
+	fadeIn: { opacity: "show" },
+	fadeOut: { opacity: "hide" },
+	fadeToggle: { opacity: "toggle" }
+}, function( name, props ) {
+	jQuery.fn[ name ] = function( speed, easing, callback ) {
+		return this.animate( props, speed, easing, callback );
+	};
+});
+
+jQuery.timers = [];
+jQuery.fx.tick = function() {
+	var timer,
+		timers = jQuery.timers,
+		i = 0;
+
+	fxNow = jQuery.now();
+
+	for ( ; i < timers.length; i++ ) {
+		timer = timers[ i ];
+		// Checks the timer has not already been removed
+		if ( !timer() && timers[ i ] === timer ) {
+			timers.splice( i--, 1 );
+		}
+	}
+
+	if ( !timers.length ) {
+		jQuery.fx.stop();
+	}
+	fxNow = undefined;
+};
+
+jQuery.fx.timer = function( timer ) {
+	jQuery.timers.push( timer );
+	if ( timer() ) {
+		jQuery.fx.start();
+	} else {
+		jQuery.timers.pop();
+	}
+};
+
+jQuery.fx.interval = 13;
+
+jQuery.fx.start = function() {
+	if ( !timerId ) {
+		timerId = setInterval( jQuery.fx.tick, jQuery.fx.interval );
+	}
+};
+
+jQuery.fx.stop = function() {
+	clearInterval( timerId );
+	timerId = null;
+};
+
+jQuery.fx.speeds = {
+	slow: 600,
+	fast: 200,
+	// Default speed
+	_default: 400
+};
+
+
+// Based off of the plugin by Clint Helfers, with permission.
+// http://blindsignals.com/index.php/2009/07/jquery-delay/
+jQuery.fn.delay = function( time, type ) {
+	time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
+	type = type || "fx";
+
+	return this.queue( type, function( next, hooks ) {
+		var timeout = setTimeout( next, time );
+		hooks.stop = function() {
+			clearTimeout( timeout );
+		};
+	});
+};
+
+
+(function() {
+	// Minified: var a,b,c,d,e
+	var input, div, select, a, opt;
+
+	// Setup
+	div = document.createElement( "div" );
+	div.setAttribute( "className", "t" );
+	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
+	a = div.getElementsByTagName("a")[ 0 ];
+
+	// First batch of tests.
+	select = document.createElement("select");
+	opt = select.appendChild( document.createElement("option") );
+	input = div.getElementsByTagName("input")[ 0 ];
+
+	a.style.cssText = "top:1px";
+
+	// Test setAttribute on camelCase class. If it works, we need attrFixes when doing get/setAttribute (ie6/7)
+	support.getSetAttribute = div.className !== "t";
+
+	// Get the style information from getAttribute
+	// (IE uses .cssText instead)
+	support.style = /top/.test( a.getAttribute("style") );
+
+	// Make sure that URLs aren't manipulated
+	// (IE normalizes it by default)
+	support.hrefNormalized = a.getAttribute("href") === "/a";
+
+	// Check the default checkbox/radio value ("" on WebKit; "on" elsewhere)
+	support.checkOn = !!input.value;
+
+	// Make sure that a selected-by-default option has a working selected property.
+	// (WebKit defaults to false instead of true, IE too, if it's in an optgroup)
+	support.optSelected = opt.selected;
+
+	// Tests for enctype support on a form (#6743)
+	support.enctype = !!document.createElement("form").enctype;
+
+	// Make sure that the options inside disabled selects aren't marked as disabled
+	// (WebKit marks them as disabled)
+	select.disabled = true;
+	support.optDisabled = !opt.disabled;
+
+	// Support: IE8 only
+	// Check if we can trust getAttribute("value")
+	input = document.createElement( "input" );
+	input.setAttribute( "value", "" );
+	support.input = input.getAttribute( "value" ) === "";
+
+	// Check if an input maintains its value after becoming a radio
+	input.value = "t";
+	input.setAttribute( "type", "radio" );
+	support.radioValue = input.value === "t";
+})();
+
+
+var rreturn = /\r/g;
+
+jQuery.fn.extend({
+	val: function( value ) {
+		var hooks, ret, isFunction,
+			elem = this[0];
+
+		if ( !arguments.length ) {
+			if ( elem ) {
+				hooks = jQuery.valHooks[ elem.type ] || jQuery.valHooks[ elem.nodeName.toLowerCase() ];
+
+				if ( hooks && "get" in hooks && (ret = hooks.get( elem, "value" )) !== undefined ) {
+					return ret;
+				}
+
+				ret = elem.value;
+
+				return typeof ret === "string" ?
+					// handle most common string cases
+					ret.replace(rreturn, "") :
+					// handle cases where value is null/undef or number
+					ret == null ? "" : ret;
+			}
+
+			return;
+		}
+
+		isFunction = jQuery.isFunction( value );
+
+		return this.each(function( i ) {
+			var val;
+
+			if ( this.nodeType !== 1 ) {
+				return;
+			}
+
+			if ( isFunction ) {
+				val = value.call( this, i, jQuery( this ).val() );
+			} else {
+				val = value;
+			}
+
+			// Treat null/undefined as ""; convert numbers to string
+			if ( val == null ) {
+				val = "";
+			} else if ( typeof val === "number" ) {
+				val += "";
+			} else if ( jQuery.isArray( val ) ) {
+				val = jQuery.map( val, function( value ) {
+					return value == null ? "" : value + "";
+				});
+			}
+
+			hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
+
+			// If set returns undefined, fall back to normal setting
+			if ( !hooks || !("set" in hooks) || hooks.set( this, val, "value" ) === undefined ) {
+				this.value = val;
+			}
+		});
+	}
+});
+
+jQuery.extend({
+	valHooks: {
+		option: {
+			get: function( elem ) {
+				var val = jQuery.find.attr( elem, "value" );
+				return val != null ?
+					val :
+					// Support: IE10-11+
+					// option.text throws exceptions (#14686, #14858)
+					jQuery.trim( jQuery.text( elem ) );
+			}
+		},
+		select: {
+			get: function( elem ) {
+				var value, option,
+					options = elem.options,
+					index = elem.selectedIndex,
+					one = elem.type === "select-one" || index < 0,
+					values = one ? null : [],
+					max = one ? index + 1 : options.length,
+					i = index < 0 ?
+						max :
+						one ? index : 0;
+
+				// Loop through all the selected options
+				for ( ; i < max; i++ ) {
+					option = options[ i ];
+
+					// oldIE doesn't update selected after form reset (#2551)
+					if ( ( option.selected || i === index ) &&
+							// Don't return options that are disabled or in a disabled optgroup
+							( support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null ) &&
+							( !option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" ) ) ) {
+
+						// Get the specific value for the option
+						value = jQuery( option ).val();
+
+						// We don't need an array for one selects
+						if ( one ) {
+							return value;
+						}
+
+						// Multi-Selects return an array
+						values.push( value );
+					}
+				}
+
+				return values;
+			},
+
+			set: function( elem, value ) {
+				var optionSet, option,
+					options = elem.options,
+					values = jQuery.makeArray( value ),
+					i = options.length;
+
+				while ( i-- ) {
+					option = options[ i ];
+
+					if ( jQuery.inArray( jQuery.valHooks.option.get( option ), values ) >= 0 ) {
+
+						// Support: IE6
+						// When new option element is added to select box we need to
+						// force reflow of newly added node in order to workaround delay
+						// of initialization properties
+						try {
+							option.selected = optionSet = true;
+
+						} catch ( _ ) {
+
+							// Will be executed only in IE6
+							option.scrollHeight;
+						}
+
+					} else {
+						option.selected = false;
+					}
+				}
+
+				// Force browsers to behave consistently when non-matching value is set
+				if ( !optionSet ) {
+					elem.selectedIndex = -1;
+				}
+
+				return options;
+			}
+		}
+	}
+});
+
+// Radios and checkboxes getter/setter
+jQuery.each([ "radio", "checkbox" ], function() {
+	jQuery.valHooks[ this ] = {
+		set: function( elem, value ) {
+			if ( jQuery.isArray( value ) ) {
+				return ( elem.checked = jQuery.inArray( jQuery(elem).val(), value ) >= 0 );
+			}
+		}
+	};
+	if ( !support.checkOn ) {
+		jQuery.valHooks[ this ].get = function( elem ) {
+			// Support: Webkit
+			// "" is returned instead of "on" if a value isn't specified
+			return elem.getAttribute("value") === null ? "on" : elem.value;
+		};
+	}
+});
+
+
+
+
+var nodeHook, boolHook,
+	attrHandle = jQuery.expr.attrHandle,
+	ruseDefault = /^(?:checked|selected)$/i,
+	getSetAttribute = support.getSetAttribute,
+	getSetInput = support.input;
+
+jQuery.fn.extend({
+	attr: function( name, value ) {
+		return access( this, jQuery.attr, name, value, arguments.length > 1 );
+	},
+
+	removeAttr: function( name ) {
+		return this.each(function() {
+			jQuery.removeAttr( this, name );
+		});
+	}
+});
+
+jQuery.extend({
+	attr: function( elem, name, value ) {
+		var hooks, ret,
+			nType = elem.nodeType;
+
+		// don't get/set attributes on text, comment and attribute nodes
+		if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
+			return;
+		}
+
+		// Fallback to prop when attributes are not supported
+		if ( typeof elem.getAttribute === strundefined ) {
+			return jQuery.prop( elem, name, value );
+		}
+
+		// All attributes are lowercase
+		// Grab necessary hook if one is defined
+		if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
+			name = name.toLowerCase();
+			hooks = jQuery.attrHooks[ name ] ||
+				( jQuery.expr.match.bool.test( name ) ? boolHook : nodeHook );
+		}
+
+		if ( value !== undefined ) {
+
+			if ( value === null ) {
+				jQuery.removeAttr( elem, name );
+
+			} else if ( hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) {
+				return ret;
+
+			} else {
+				elem.setAttribute( name, value + "" );
+				return value;
+			}
+
+		} else if ( hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) {
+			return ret;
+
+		} else {
+			ret = jQuery.find.attr( elem, name );
+
+			// Non-existent attributes return null, we normalize to undefined
+			return ret == null ?
+				undefined :
+				ret;
+		}
+	},
+
+	removeAttr: function( elem, value ) {
+		var name, propName,
+			i = 0,
+			attrNames = value && value.match( rnotwhite );
+
+		if ( attrNames && elem.nodeType === 1 ) {
+			while ( (name = attrNames[i++]) ) {
+				propName = jQuery.propFix[ name ] || name;
+
+				// Boolean attributes get special treatment (#10870)
+				if ( jQuery.expr.match.bool.test( name ) ) {
+					// Set corresponding property to false
+					if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) {
+						elem[ propName ] = false;
+					// Support: IE<9
+					// Also clear defaultChecked/defaultSelected (if appropriate)
+					} else {
+						elem[ jQuery.camelCase( "default-" + name ) ] =
+							elem[ propName ] = false;
+					}
+
+				// See #9699 for explanation of this approach (setting first, then removal)
+				} else {
+					jQuery.attr( elem, name, "" );
+				}
+
+				elem.removeAttribute( getSetAttribute ? name : propName );
+			}
+		}
+	},
+
+	attrHooks: {
+		type: {
+			set: function( elem, value ) {
+				if ( !support.radioValue && value === "radio" && jQuery.nodeName(elem, "input") ) {
+					// Setting the type on a radio button after the value resets the value in IE6-9
+					// Reset value to default in case type is set after value during creation
+					var val = elem.value;
+					elem.setAttribute( "type", value );
+					if ( val ) {
+						elem.value = val;
+					}
+					return value;
+				}
+			}
+		}
+	}
+});
+
+// Hook for boolean attributes
+boolHook = {
+	set: function( elem, value, name ) {
+		if ( value === false ) {
+			// Remove boolean attributes when set to false
+			jQuery.removeAttr( elem, name );
+		} else if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) {
+			// IE<8 needs the *property* name
+			elem.setAttribute( !getSetAttribute && jQuery.propFix[ name ] || name, name );
+
+		// Use defaultChecked and defaultSelected for oldIE
+		} else {
+			elem[ jQuery.camelCase( "default-" + name ) ] = elem[ name ] = true;
+		}
+
+		return name;
+	}
+};
+
+// Retrieve booleans specially
+jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) {
+
+	var getter = attrHandle[ name ] || jQuery.find.attr;
+
+	attrHandle[ name ] = getSetInput && getSetAttribute || !ruseDefault.test( name ) ?
+		function( elem, name, isXML ) {
+			var ret, handle;
+			if ( !isXML ) {
+				// Avoid an infinite loop by temporarily removing this function from the getter
+				handle = attrHandle[ name ];
+				attrHandle[ name ] = ret;
+				ret = getter( elem, name, isXML ) != null ?
+					name.toLowerCase() :
+					null;
+				attrHandle[ name ] = handle;
+			}
+			return ret;
+		} :
+		function( elem, name, isXML ) {
+			if ( !isXML ) {
+				return elem[ jQuery.camelCase( "default-" + name ) ] ?
+					name.toLowerCase() :
+					null;
+			}
+		};
+});
+
+// fix oldIE attroperties
+if ( !getSetInput || !getSetAttribute ) {
+	jQuery.attrHooks.value = {
+		set: function( elem, value, name ) {
+			if ( jQuery.nodeName( elem, "input" ) ) {
+				// Does not return so that setAttribute is also used
+				elem.defaultValue = value;
+			} else {
+				// Use nodeHook if defined (#1954); otherwise setAttribute is fine
+				return nodeHook && nodeHook.set( elem, value, name );
+			}
+		}
+	};
+}
+
+// IE6/7 do not support getting/setting some attributes with get/setAttribute
+if ( !getSetAttribute ) {
+
+	// Use this for any attribute in IE6/7
+	// This fixes almost every IE6/7 issue
+	nodeHook = {
+		set: function( elem, value, name ) {
+			// Set the existing or create a new attribute node
+			var ret = elem.getAttributeNode( name );
+			if ( !ret ) {
+				elem.setAttributeNode(
+					(ret = elem.ownerDocument.createAttribute( name ))
+				);
+			}
+
+			ret.value = value += "";
+
+			// Break association with cloned elements by also using setAttribute (#9646)
+			if ( name === "value" || value === elem.getAttribute( name ) ) {
+				return value;
+			}
+		}
+	};
+
+	// Some attributes are constructed with empty-string values when not defined
+	attrHandle.id = attrHandle.name = attrHandle.coords =
+		function( elem, name, isXML ) {
+			var ret;
+			if ( !isXML ) {
+				return (ret = elem.getAttributeNode( name )) && ret.value !== "" ?
+					ret.value :
+					null;
+			}
+		};
+
+	// Fixing value retrieval on a button requires this module
+	jQuery.valHooks.button = {
+		get: function( elem, name ) {
+			var ret = elem.getAttributeNode( name );
+			if ( ret && ret.specified ) {
+				return ret.value;
+			}
+		},
+		set: nodeHook.set
+	};
+
+	// Set contenteditable to false on removals(#10429)
+	// Setting to empty string throws an error as an invalid value
+	jQuery.attrHooks.contenteditable = {
+		set: function( elem, value, name ) {
+			nodeHook.set( elem, value === "" ? false : value, name );
+		}
+	};
+
+	// Set width and height to auto instead of 0 on empty string( Bug #8150 )
+	// This is for removals
+	jQuery.each([ "width", "height" ], function( i, name ) {
+		jQuery.attrHooks[ name ] = {
+			set: function( elem, value ) {
+				if ( value === "" ) {
+					elem.setAttribute( name, "auto" );
+					return value;
+				}
+			}
+		};
+	});
+}
+
+if ( !support.style ) {
+	jQuery.attrHooks.style = {
+		get: function( elem ) {
+			// Return undefined in the case of empty string
+			// Note: IE uppercases css property names, but if we were to .toLowerCase()
+			// .cssText, that would destroy case senstitivity in URL's, like in "background"
+			return elem.style.cssText || undefined;
+		},
+		set: function( elem, value ) {
+			return ( elem.style.cssText = value + "" );
+		}
+	};
+}
+
+
+
+
+var rfocusable = /^(?:input|select|textarea|button|object)$/i,
+	rclickable = /^(?:a|area)$/i;
+
+jQuery.fn.extend({
+	prop: function( name, value ) {
+		return access( this, jQuery.prop, name, value, arguments.length > 1 );
+	},
+
+	removeProp: function( name ) {
+		name = jQuery.propFix[ name ] || name;
+		return this.each(function() {
+			// try/catch handles cases where IE balks (such as removing a property on window)
+			try {
+				this[ name ] = undefined;
+				delete this[ name ];
+			} catch( e ) {}
+		});
+	}
+});
+
+jQuery.extend({
+	propFix: {
+		"for": "htmlFor",
+		"class": "className"
+	},
+
+	prop: function( elem, name, value ) {
+		var ret, hooks, notxml,
+			nType = elem.nodeType;
+
+		// don't get/set properties on text, comment and attribute nodes
+		if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
+			return;
+		}
+
+		notxml = nType !== 1 || !jQuery.isXMLDoc( elem );
+
+		if ( notxml ) {
+			// Fix name and attach hooks
+			name = jQuery.propFix[ name ] || name;
+			hooks = jQuery.propHooks[ name ];
+		}
+
+		if ( value !== undefined ) {
+			return hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ?
+				ret :
+				( elem[ name ] = value );
+
+		} else {
+			return hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ?
+				ret :
+				elem[ name ];
+		}
+	},
+
+	propHooks: {
+		tabIndex: {
+			get: function( elem ) {
+				// elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set
+				// http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
+				// Use proper attribute retrieval(#12072)
+				var tabindex = jQuery.find.attr( elem, "tabindex" );
+
+				return tabindex ?
+					parseInt( tabindex, 10 ) :
+					rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ?
+						0 :
+						-1;
+			}
+		}
+	}
+});
+
+// Some attributes require a special call on IE
+// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
+if ( !support.hrefNormalized ) {
+	// href/src property should get the full normalized URL (#10299/#12915)
+	jQuery.each([ "href", "src" ], function( i, name ) {
+		jQuery.propHooks[ name ] = {
+			get: function( elem ) {
+				return elem.getAttribute( name, 4 );
+			}
+		};
+	});
+}
+
+// Support: Safari, IE9+
+// mis-reports the default selected property of an option
+// Accessing the parent's selectedIndex property fixes it
+if ( !support.optSelected ) {
+	jQuery.propHooks.selected = {
+		get: function( elem ) {
+			var parent = elem.parentNode;
+
+			if ( parent ) {
+				parent.selectedIndex;
+
+				// Make sure that it also works with optgroups, see #5701
+				if ( parent.parentNode ) {
+					parent.parentNode.selectedIndex;
+				}
+			}
+			return null;
+		}
+	};
+}
+
+jQuery.each([
+	"tabIndex",
+	"readOnly",
+	"maxLength",
+	"cellSpacing",
+	"cellPadding",
+	"rowSpan",
+	"colSpan",
+	"useMap",
+	"frameBorder",
+	"contentEditable"
+], function() {
+	jQuery.propFix[ this.toLowerCase() ] = this;
+});
+
+// IE6/7 call enctype encoding
+if ( !support.enctype ) {
+	jQuery.propFix.enctype = "encoding";
+}
+
+
+
+
+var rclass = /[\t\r\n\f]/g;
+
+jQuery.fn.extend({
+	addClass: function( value ) {
+		var classes, elem, cur, clazz, j, finalValue,
+			i = 0,
+			len = this.length,
+			proceed = typeof value === "string" && value;
+
+		if ( jQuery.isFunction( value ) ) {
+			return this.each(function( j ) {
+				jQuery( this ).addClass( value.call( this, j, this.className ) );
+			});
+		}
+
+		if ( proceed ) {
+			// The disjunction here is for better compressibility (see removeClass)
+			classes = ( value || "" ).match( rnotwhite ) || [];
+
+			for ( ; i < len; i++ ) {
+				elem = this[ i ];
+				cur = elem.nodeType === 1 && ( elem.className ?
+					( " " + elem.className + " " ).replace( rclass, " " ) :
+					" "
+				);
+
+				if ( cur ) {
+					j = 0;
+					while ( (clazz = classes[j++]) ) {
+						if ( cur.indexOf( " " + clazz + " " ) < 0 ) {
+							cur += clazz + " ";
+						}
+					}
+
+					// only assign if different to avoid unneeded rendering.
+					finalValue = jQuery.trim( cur );
+					if ( elem.className !== finalValue ) {
+						elem.className = finalValue;
+					}
+				}
+			}
+		}
+
+		return this;
+	},
+
+	removeClass: function( value ) {
+		var classes, elem, cur, clazz, j, finalValue,
+			i = 0,
+			len = this.length,
+			proceed = arguments.length === 0 || typeof value === "string" && value;
+
+		if ( jQuery.isFunction( value ) ) {
+			return this.each(function( j ) {
+				jQuery( this ).removeClass( value.call( this, j, this.className ) );
+			});
+		}
+		if ( proceed ) {
+			classes = ( value || "" ).match( rnotwhite ) || [];
+
+			for ( ; i < len; i++ ) {
+				elem = this[ i ];
+				// This expression is here for better compressibility (see addClass)
+				cur = elem.nodeType === 1 && ( elem.className ?
+					( " " + elem.className + " " ).replace( rclass, " " ) :
+					""
+				);
+
+				if ( cur ) {
+					j = 0;
+					while ( (clazz = classes[j++]) ) {
+						// Remove *all* instances
+						while ( cur.indexOf( " " + clazz + " " ) >= 0 ) {
+							cur = cur.replace( " " + clazz + " ", " " );
+						}
+					}
+
+					// only assign if different to avoid unneeded rendering.
+					finalValue = value ? jQuery.trim( cur ) : "";
+					if ( elem.className !== finalValue ) {
+						elem.className = finalValue;
+					}
+				}
+			}
+		}
+
+		return this;
+	},
+
+	toggleClass: function( value, stateVal ) {
+		var type = typeof value;
+
+		if ( typeof stateVal === "boolean" && type === "string" ) {
+			return stateVal ? this.addClass( value ) : this.removeClass( value );
+		}
+
+		if ( jQuery.isFunction( value ) ) {
+			return this.each(function( i ) {
+				jQuery( this ).toggleClass( value.call(this, i, this.className, stateVal), stateVal );
+			});
+		}
+
+		return this.each(function() {
+			if ( type === "string" ) {
+				// toggle individual class names
+				var className,
+					i = 0,
+					self = jQuery( this ),
+					classNames = value.match( rnotwhite ) || [];
+
+				while ( (className = classNames[ i++ ]) ) {
+					// check each className given, space separated list
+					if ( self.hasClass( className ) ) {
+						self.removeClass( className );
+					} else {
+						self.addClass( className );
+					}
+				}
+
+			// Toggle whole class name
+			} else if ( type === strundefined || type === "boolean" ) {
+				if ( this.className ) {
+					// store className if set
+					jQuery._data( this, "__className__", this.className );
+				}
+
+				// If the element has a class name or if we're passed "false",
+				// then remove the whole classname (if there was one, the above saved it).
+				// Otherwise bring back whatever was previously saved (if anything),
+				// falling back to the empty string if nothing was stored.
+				this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || "";
+			}
+		});
+	},
+
+	hasClass: function( selector ) {
+		var className = " " + selector + " ",
+			i = 0,
+			l = this.length;
+		for ( ; i < l; i++ ) {
+			if ( this[i].nodeType === 1 && (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) >= 0 ) {
+				return true;
+			}
+		}
+
+		return false;
+	}
+});
+
+
+
+
+// Return jQuery for attributes-only inclusion
+
+
+jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " +
+	"mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
+	"change select submit keydown keypress keyup error contextmenu").split(" "), function( i, name ) {
+
+	// Handle event binding
+	jQuery.fn[ name ] = function( data, fn ) {
+		return arguments.length > 0 ?
+			this.on( name, null, data, fn ) :
+			this.trigger( name );
+	};
+});
+
+jQuery.fn.extend({
+	hover: function( fnOver, fnOut ) {
+		return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
+	},
+
+	bind: function( types, data, fn ) {
+		return this.on( types, null, data, fn );
+	},
+	unbind: function( types, fn ) {
+		return this.off( types, null, fn );
+	},
+
+	delegate: function( selector, types, data, fn ) {
+		return this.on( types, selector, data, fn );
+	},
+	undelegate: function( selector, types, fn ) {
+		// ( namespace ) or ( selector, types [, fn] )
+		return arguments.length === 1 ? this.off( selector, "**" ) : this.off( types, selector || "**", fn );
+	}
+});
+
+
+var nonce = jQuery.now();
+
+var rquery = (/\?/);
+
+
+
+var rvalidtokens = /(,)|(\[|{)|(}|])|"(?:[^"\\\r\n]|\\["\\\/bfnrt]|\\u[\da-fA-F]{4})*"\s*:?|true|false|null|-?(?!0\d)\d+(?:\.\d+|)(?:[eE][+-]?\d+|)/g;
+
+jQuery.parseJSON = function( data ) {
+	// Attempt to parse using the native JSON parser first
+	if ( window.JSON && window.JSON.parse ) {
+		// Support: Android 2.3
+		// Workaround failure to string-cast null input
+		return window.JSON.parse( data + "" );
+	}
+
+	var requireNonComma,
+		depth = null,
+		str = jQuery.trim( data + "" );
+
+	// Guard against invalid (and possibly dangerous) input by ensuring that nothing remains
+	// after removing valid tokens
+	return str && !jQuery.trim( str.replace( rvalidtokens, function( token, comma, open, close ) {
+
+		// Force termination if we see a misplaced comma
+		if ( requireNonComma && comma ) {
+			depth = 0;
+		}
+
+		// Perform no more replacements after returning to outermost depth
+		if ( depth === 0 ) {
+			return token;
+		}
+
+		// Commas must not follow "[", "{", or ","
+		requireNonComma = open || comma;
+
+		// Determine new depth
+		// array/object open ("[" or "{"): depth += true - false (increment)
+		// array/object close ("]" or "}"): depth += false - true (decrement)
+		// other cases ("," or primitive): depth += true - true (numeric cast)
+		depth += !close - !open;
+
+		// Remove this token
+		return "";
+	}) ) ?
+		( Function( "return " + str ) )() :
+		jQuery.error( "Invalid JSON: " + data );
+};
+
+
+// Cross-browser xml parsing
+jQuery.parseXML = function( data ) {
+	var xml, tmp;
+	if ( !data || typeof data !== "string" ) {
+		return null;
+	}
+	try {
+		if ( window.DOMParser ) { // Standard
+			tmp = new DOMParser();
+			xml = tmp.parseFromString( data, "text/xml" );
+		} else { // IE
+			xml = new ActiveXObject( "Microsoft.XMLDOM" );
+			xml.async = "false";
+			xml.loadXML( data );
+		}
+	} catch( e ) {
+		xml = undefined;
+	}
+	if ( !xml || !xml.documentElement || xml.getElementsByTagName( "parsererror" ).length ) {
+		jQuery.error( "Invalid XML: " + data );
+	}
+	return xml;
+};
+
+
+var
+	// Document location
+	ajaxLocParts,
+	ajaxLocation,
+
+	rhash = /#.*$/,
+	rts = /([?&])_=[^&]*/,
+	rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL
+	// #7653, #8125, #8152: local protocol detection
+	rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/,
+	rnoContent = /^(?:GET|HEAD)$/,
+	rprotocol = /^\/\//,
+	rurl = /^([\w.+-]+:)(?:\/\/(?:[^\/?#]*@|)([^\/?#:]*)(?::(\d+)|)|)/,
+
+	/* Prefilters
+	 * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
+	 * 2) These are called:
+	 *    - BEFORE asking for a transport
+	 *    - AFTER param serialization (s.data is a string if s.processData is true)
+	 * 3) key is the dataType
+	 * 4) the catchall symbol "*" can be used
+	 * 5) execution will start with transport dataType and THEN continue down to "*" if needed
+	 */
+	prefilters = {},
+
+	/* Transports bindings
+	 * 1) key is the dataType
+	 * 2) the catchall symbol "*" can be used
+	 * 3) selection will start with transport dataType and THEN go to "*" if needed
+	 */
+	transports = {},
+
+	// Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
+	allTypes = "*/".concat("*");
+
+// #8138, IE may throw an exception when accessing
+// a field from window.location if document.domain has been set
+try {
+	ajaxLocation = location.href;
+} catch( e ) {
+	// Use the href attribute of an A element
+	// since IE will modify it given document.location
+	ajaxLocation = document.createElement( "a" );
+	ajaxLocation.href = "";
+	ajaxLocation = ajaxLocation.href;
+}
+
+// Segment location into parts
+ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || [];
+
+// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
+function addToPrefiltersOrTransports( structure ) {
+
+	// dataTypeExpression is optional and defaults to "*"
+	return function( dataTypeExpression, func ) {
+
+		if ( typeof dataTypeExpression !== "string" ) {
+			func = dataTypeExpression;
+			dataTypeExpression = "*";
+		}
+
+		var dataType,
+			i = 0,
+			dataTypes = dataTypeExpression.toLowerCase().match( rnotwhite ) || [];
+
+		if ( jQuery.isFunction( func ) ) {
+			// For each dataType in the dataTypeExpression
+			while ( (dataType = dataTypes[i++]) ) {
+				// Prepend if requested
+				if ( dataType.charAt( 0 ) === "+" ) {
+					dataType = dataType.slice( 1 ) || "*";
+					(structure[ dataType ] = structure[ dataType ] || []).unshift( func );
+
+				// Otherwise append
+				} else {
+					(structure[ dataType ] = structure[ dataType ] || []).push( func );
+				}
+			}
+		}
+	};
+}
+
+// Base inspection function for prefilters and transports
+function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) {
+
+	var inspected = {},
+		seekingTransport = ( structure === transports );
+
+	function inspect( dataType ) {
+		var selected;
+		inspected[ dataType ] = true;
+		jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) {
+			var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR );
+			if ( typeof dataTypeOrTransport === "string" && !seekingTransport && !inspected[ dataTypeOrTransport ] ) {
+				options.dataTypes.unshift( dataTypeOrTransport );
+				inspect( dataTypeOrTransport );
+				return false;
+			} else if ( seekingTransport ) {
+				return !( selected = dataTypeOrTransport );
+			}
+		});
+		return selected;
+	}
+
+	return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" );
+}
+
+// A special extend for ajax options
+// that takes "flat" options (not to be deep extended)
+// Fixes #9887
+function ajaxExtend( target, src ) {
+	var deep, key,
+		flatOptions = jQuery.ajaxSettings.flatOptions || {};
+
+	for ( key in src ) {
+		if ( src[ key ] !== undefined ) {
+			( flatOptions[ key ] ? target : ( deep || (deep = {}) ) )[ key ] = src[ key ];
+		}
+	}
+	if ( deep ) {
+		jQuery.extend( true, target, deep );
+	}
+
+	return target;
+}
+
+/* Handles responses to an ajax request:
+ * - finds the right dataType (mediates between content-type and expected dataType)
+ * - returns the corresponding response
+ */
+function ajaxHandleResponses( s, jqXHR, responses ) {
+	var firstDataType, ct, finalDataType, type,
+		contents = s.contents,
+		dataTypes = s.dataTypes;
+
+	// Remove auto dataType and get content-type in the process
+	while ( dataTypes[ 0 ] === "*" ) {
+		dataTypes.shift();
+		if ( ct === undefined ) {
+			ct = s.mimeType || jqXHR.getResponseHeader("Content-Type");
+		}
+	}
+
+	// Check if we're dealing with a known content-type
+	if ( ct ) {
+		for ( type in contents ) {
+			if ( contents[ type ] && contents[ type ].test( ct ) ) {
+				dataTypes.unshift( type );
+				break;
+			}
+		}
+	}
+
+	// Check to see if we have a response for the expected dataType
+	if ( dataTypes[ 0 ] in responses ) {
+		finalDataType = dataTypes[ 0 ];
+	} else {
+		// Try convertible dataTypes
+		for ( type in responses ) {
+			if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[0] ] ) {
+				finalDataType = type;
+				break;
+			}
+			if ( !firstDataType ) {
+				firstDataType = type;
+			}
+		}
+		// Or just use first one
+		finalDataType = finalDataType || firstDataType;
+	}
+
+	// If we found a dataType
+	// We add the dataType to the list if needed
+	// and return the corresponding response
+	if ( finalDataType ) {
+		if ( finalDataType !== dataTypes[ 0 ] ) {
+			dataTypes.unshift( finalDataType );
+		}
+		return responses[ finalDataType ];
+	}
+}
+
+/* Chain conversions given the request and the original response
+ * Also sets the responseXXX fields on the jqXHR instance
+ */
+function ajaxConvert( s, response, jqXHR, isSuccess ) {
+	var conv2, current, conv, tmp, prev,
+		converters = {},
+		// Work with a copy of dataTypes in case we need to modify it for conversion
+		dataTypes = s.dataTypes.slice();
+
+	// Create converters map with lowercased keys
+	if ( dataTypes[ 1 ] ) {
+		for ( conv in s.converters ) {
+			converters[ conv.toLowerCase() ] = s.converters[ conv ];
+		}
+	}
+
+	current = dataTypes.shift();
+
+	// Convert to each sequential dataType
+	while ( current ) {
+
+		if ( s.responseFields[ current ] ) {
+			jqXHR[ s.responseFields[ current ] ] = response;
+		}
+
+		// Apply the dataFilter if provided
+		if ( !prev && isSuccess && s.dataFilter ) {
+			response = s.dataFilter( response, s.dataType );
+		}
+
+		prev = current;
+		current = dataTypes.shift();
+
+		if ( current ) {
+
+			// There's only work to do if current dataType is non-auto
+			if ( current === "*" ) {
+
+				current = prev;
+
+			// Convert response if prev dataType is non-auto and differs from current
+			} else if ( prev !== "*" && prev !== current ) {
+
+				// Seek a direct converter
+				conv = converters[ prev + " " + current ] || converters[ "* " + current ];
+
+				// If none found, seek a pair
+				if ( !conv ) {
+					for ( conv2 in converters ) {
+
+						// If conv2 outputs current
+						tmp = conv2.split( " " );
+						if ( tmp[ 1 ] === current ) {
+
+							// If prev can be converted to accepted input
+							conv = converters[ prev + " " + tmp[ 0 ] ] ||
+								converters[ "* " + tmp[ 0 ] ];
+							if ( conv ) {
+								// Condense equivalence converters
+								if ( conv === true ) {
+									conv = converters[ conv2 ];
+
+								// Otherwise, insert the intermediate dataType
+								} else if ( converters[ conv2 ] !== true ) {
+									current = tmp[ 0 ];
+									dataTypes.unshift( tmp[ 1 ] );
+								}
+								break;
+							}
+						}
+					}
+				}
+
+				// Apply converter (if not an equivalence)
+				if ( conv !== true ) {
+
+					// Unless errors are allowed to bubble, catch and return them
+					if ( conv && s[ "throws" ] ) {
+						response = conv( response );
+					} else {
+						try {
+							response = conv( response );
+						} catch ( e ) {
+							return { state: "parsererror", error: conv ? e : "No conversion from " + prev + " to " + current };
+						}
+					}
+				}
+			}
+		}
+	}
+
+	return { state: "success", data: response };
+}
+
+jQuery.extend({
+
+	// Counter for holding the number of active queries
+	active: 0,
+
+	// Last-Modified header cache for next request
+	lastModified: {},
+	etag: {},
+
+	ajaxSettings: {
+		url: ajaxLocation,
+		type: "GET",
+		isLocal: rlocalProtocol.test( ajaxLocParts[ 1 ] ),
+		global: true,
+		processData: true,
+		async: true,
+		contentType: "application/x-www-form-urlencoded; charset=UTF-8",
+		/*
+		timeout: 0,
+		data: null,
+		dataType: null,
+		username: null,
+		password: null,
+		cache: null,
+		throws: false,
+		traditional: false,
+		headers: {},
+		*/
+
+		accepts: {
+			"*": allTypes,
+			text: "text/plain",
+			html: "text/html",
+			xml: "application/xml, text/xml",
+			json: "application/json, text/javascript"
+		},
+
+		contents: {
+			xml: /xml/,
+			html: /html/,
+			json: /json/
+		},
+
+		responseFields: {
+			xml: "responseXML",
+			text: "responseText",
+			json: "responseJSON"
+		},
+
+		// Data converters
+		// Keys separate source (or catchall "*") and destination types with a single space
+		converters: {
+
+			// Convert anything to text
+			"* text": String,
+
+			// Text to html (true = no transformation)
+			"text html": true,
+
+			// Evaluate text as a json expression
+			"text json": jQuery.parseJSON,
+
+			// Parse text as xml
+			"text xml": jQuery.parseXML
+		},
+
+		// For options that shouldn't be deep extended:
+		// you can add your own custom options here if
+		// and when you create one that shouldn't be
+		// deep extended (see ajaxExtend)
+		flatOptions: {
+			url: true,
+			context: true
+		}
+	},
+
+	// Creates a full fledged settings object into target
+	// with both ajaxSettings and settings fields.
+	// If target is omitted, writes into ajaxSettings.
+	ajaxSetup: function( target, settings ) {
+		return settings ?
+
+			// Building a settings object
+			ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) :
+
+			// Extending ajaxSettings
+			ajaxExtend( jQuery.ajaxSettings, target );
+	},
+
+	ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
+	ajaxTransport: addToPrefiltersOrTransports( transports ),
+
+	// Main method
+	ajax: function( url, options ) {
+
+		// If url is an object, simulate pre-1.5 signature
+		if ( typeof url === "object" ) {
+			options = url;
+			url = undefined;
+		}
+
+		// Force options to be an object
+		options = options || {};
+
+		var // Cross-domain detection vars
+			parts,
+			// Loop variable
+			i,
+			// URL without anti-cache param
+			cacheURL,
+			// Response headers as string
+			responseHeadersString,
+			// timeout handle
+			timeoutTimer,
+
+			// To know if global events are to be dispatched
+			fireGlobals,
+
+			transport,
+			// Response headers
+			responseHeaders,
+			// Create the final options object
+			s = jQuery.ajaxSetup( {}, options ),
+			// Callbacks context
+			callbackContext = s.context || s,
+			// Context for global events is callbackContext if it is a DOM node or jQuery collection
+			globalEventContext = s.context && ( callbackContext.nodeType || callbackContext.jquery ) ?
+				jQuery( callbackContext ) :
+				jQuery.event,
+			// Deferreds
+			deferred = jQuery.Deferred(),
+			completeDeferred = jQuery.Callbacks("once memory"),
+			// Status-dependent callbacks
+			statusCode = s.statusCode || {},
+			// Headers (they are sent all at once)
+			requestHeaders = {},
+			requestHeadersNames = {},
+			// The jqXHR state
+			state = 0,
+			// Default abort message
+			strAbort = "canceled",
+			// Fake xhr
+			jqXHR = {
+				readyState: 0,
+
+				// Builds headers hashtable if needed
+				getResponseHeader: function( key ) {
+					var match;
+					if ( state === 2 ) {
+						if ( !responseHeaders ) {
+							responseHeaders = {};
+							while ( (match = rheaders.exec( responseHeadersString )) ) {
+								responseHeaders[ match[1].toLowerCase() ] = match[ 2 ];
+							}
+						}
+						match = responseHeaders[ key.toLowerCase() ];
+					}
+					return match == null ? null : match;
+				},
+
+				// Raw string
+				getAllResponseHeaders: function() {
+					return state === 2 ? responseHeadersString : null;
+				},
+
+				// Caches the header
+				setRequestHeader: function( name, value ) {
+					var lname = name.toLowerCase();
+					if ( !state ) {
+						name = requestHeadersNames[ lname ] = requestHeadersNames[ lname ] || name;
+						requestHeaders[ name ] = value;
+					}
+					return this;
+				},
+
+				// Overrides response content-type header
+				overrideMimeType: function( type ) {
+					if ( !state ) {
+						s.mimeType = type;
+					}
+					return this;
+				},
+
+				// Status-dependent callbacks
+				statusCode: function( map ) {
+					var code;
+					if ( map ) {
+						if ( state < 2 ) {
+							for ( code in map ) {
+								// Lazy-add the new callback in a way that preserves old ones
+								statusCode[ code ] = [ statusCode[ code ], map[ code ] ];
+							}
+						} else {
+							// Execute the appropriate callbacks
+							jqXHR.always( map[ jqXHR.status ] );
+						}
+					}
+					return this;
+				},
+
+				// Cancel the request
+				abort: function( statusText ) {
+					var finalText = statusText || strAbort;
+					if ( transport ) {
+						transport.abort( finalText );
+					}
+					done( 0, finalText );
+					return this;
+				}
+			};
+
+		// Attach deferreds
+		deferred.promise( jqXHR ).complete = completeDeferred.add;
+		jqXHR.success = jqXHR.done;
+		jqXHR.error = jqXHR.fail;
+
+		// Remove hash character (#7531: and string promotion)
+		// Add protocol if not provided (#5866: IE7 issue with protocol-less urls)
+		// Handle falsy url in the settings object (#10093: consistency with old signature)
+		// We also use the url parameter if available
+		s.url = ( ( url || s.url || ajaxLocation ) + "" ).replace( rhash, "" ).replace( rprotocol, ajaxLocParts[ 1 ] + "//" );
+
+		// Alias method option to type as per ticket #12004
+		s.type = options.method || options.type || s.method || s.type;
+
+		// Extract dataTypes list
+		s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().match( rnotwhite ) || [ "" ];
+
+		// A cross-domain request is in order when we have a protocol:host:port mismatch
+		if ( s.crossDomain == null ) {
+			parts = rurl.exec( s.url.toLowerCase() );
+			s.crossDomain = !!( parts &&
+				( parts[ 1 ] !== ajaxLocParts[ 1 ] || parts[ 2 ] !== ajaxLocParts[ 2 ] ||
+					( parts[ 3 ] || ( parts[ 1 ] === "http:" ? "80" : "443" ) ) !==
+						( ajaxLocParts[ 3 ] || ( ajaxLocParts[ 1 ] === "http:" ? "80" : "443" ) ) )
+			);
+		}
+
+		// Convert data if not already a string
+		if ( s.data && s.processData && typeof s.data !== "string" ) {
+			s.data = jQuery.param( s.data, s.traditional );
+		}
+
+		// Apply prefilters
+		inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
+
+		// If request was aborted inside a prefilter, stop there
+		if ( state === 2 ) {
+			return jqXHR;
+		}
+
+		// We can fire global events as of now if asked to
+		fireGlobals = s.global;
+
+		// Watch for a new set of requests
+		if ( fireGlobals && jQuery.active++ === 0 ) {
+			jQuery.event.trigger("ajaxStart");
+		}
+
+		// Uppercase the type
+		s.type = s.type.toUpperCase();
+
+		// Determine if request has content
+		s.hasContent = !rnoContent.test( s.type );
+
+		// Save the URL in case we're toying with the If-Modified-Since
+		// and/or If-None-Match header later on
+		cacheURL = s.url;
+
+		// More options handling for requests with no content
+		if ( !s.hasContent ) {
+
+			// If data is available, append data to url
+			if ( s.data ) {
+				cacheURL = ( s.url += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data );
+				// #9682: remove data so that it's not used in an eventual retry
+				delete s.data;
+			}
+
+			// Add anti-cache in url if needed
+			if ( s.cache === false ) {
+				s.url = rts.test( cacheURL ) ?
+
+					// If there is already a '_' parameter, set its value
+					cacheURL.replace( rts, "$1_=" + nonce++ ) :
+
+					// Otherwise add one to the end
+					cacheURL + ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + nonce++;
+			}
+		}
+
+		// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+		if ( s.ifModified ) {
+			if ( jQuery.lastModified[ cacheURL ] ) {
+				jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] );
+			}
+			if ( jQuery.etag[ cacheURL ] ) {
+				jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] );
+			}
+		}
+
+		// Set the correct header, if data is being sent
+		if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
+			jqXHR.setRequestHeader( "Content-Type", s.contentType );
+		}
+
+		// Set the Accepts header for the server, depending on the dataType
+		jqXHR.setRequestHeader(
+			"Accept",
+			s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ?
+				s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
+				s.accepts[ "*" ]
+		);
+
+		// Check for headers option
+		for ( i in s.headers ) {
+			jqXHR.setRequestHeader( i, s.headers[ i ] );
+		}
+
+		// Allow custom headers/mimetypes and early abort
+		if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || state === 2 ) ) {
+			// Abort if not done already and return
+			return jqXHR.abort();
+		}
+
+		// aborting is no longer a cancellation
+		strAbort = "abort";
+
+		// Install callbacks on deferreds
+		for ( i in { success: 1, error: 1, complete: 1 } ) {
+			jqXHR[ i ]( s[ i ] );
+		}
+
+		// Get transport
+		transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
+
+		// If no transport, we auto-abort
+		if ( !transport ) {
+			done( -1, "No Transport" );
+		} else {
+			jqXHR.readyState = 1;
+
+			// Send global event
+			if ( fireGlobals ) {
+				globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
+			}
+			// Timeout
+			if ( s.async && s.timeout > 0 ) {
+				timeoutTimer = setTimeout(function() {
+					jqXHR.abort("timeout");
+				}, s.timeout );
+			}
+
+			try {
+				state = 1;
+				transport.send( requestHeaders, done );
+			} catch ( e ) {
+				// Propagate exception as error if not done
+				if ( state < 2 ) {
+					done( -1, e );
+				// Simply rethrow otherwise
+				} else {
+					throw e;
+				}
+			}
+		}
+
+		// Callback for when everything is done
+		function done( status, nativeStatusText, responses, headers ) {
+			var isSuccess, success, error, response, modified,
+				statusText = nativeStatusText;
+
+			// Called once
+			if ( state === 2 ) {
+				return;
+			}
+
+			// State is "done" now
+			state = 2;
+
+			// Clear timeout if it exists
+			if ( timeoutTimer ) {
+				clearTimeout( timeoutTimer );
+			}
+
+			// Dereference transport for early garbage collection
+			// (no matter how long the jqXHR object will be used)
+			transport = undefined;
+
+			// Cache response headers
+			responseHeadersString = headers || "";
+
+			// Set readyState
+			jqXHR.readyState = status > 0 ? 4 : 0;
+
+			// Determine if successful
+			isSuccess = status >= 200 && status < 300 || status === 304;
+
+			// Get response data
+			if ( responses ) {
+				response = ajaxHandleResponses( s, jqXHR, responses );
+			}
+
+			// Convert no matter what (that way responseXXX fields are always set)
+			response = ajaxConvert( s, response, jqXHR, isSuccess );
+
+			// If successful, handle type chaining
+			if ( isSuccess ) {
+
+				// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+				if ( s.ifModified ) {
+					modified = jqXHR.getResponseHeader("Last-Modified");
+					if ( modified ) {
+						jQuery.lastModified[ cacheURL ] = modified;
+					}
+					modified = jqXHR.getResponseHeader("etag");
+					if ( modified ) {
+						jQuery.etag[ cacheURL ] = modified;
+					}
+				}
+
+				// if no content
+				if ( status === 204 || s.type === "HEAD" ) {
+					statusText = "nocontent";
+
+				// if not modified
+				} else if ( status === 304 ) {
+					statusText = "notmodified";
+
+				// If we have data, let's convert it
+				} else {
+					statusText = response.state;
+					success = response.data;
+					error = response.error;
+					isSuccess = !error;
+				}
+			} else {
+				// We extract error from statusText
+				// then normalize statusText and status for non-aborts
+				error = statusText;
+				if ( status || !statusText ) {
+					statusText = "error";
+					if ( status < 0 ) {
+						status = 0;
+					}
+				}
+			}
+
+			// Set data for the fake xhr object
+			jqXHR.status = status;
+			jqXHR.statusText = ( nativeStatusText || statusText ) + "";
+
+			// Success/Error
+			if ( isSuccess ) {
+				deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
+			} else {
+				deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
+			}
+
+			// Status-dependent callbacks
+			jqXHR.statusCode( statusCode );
+			statusCode = undefined;
+
+			if ( fireGlobals ) {
+				globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError",
+					[ jqXHR, s, isSuccess ? success : error ] );
+			}
+
+			// Complete
+			completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
+
+			if ( fireGlobals ) {
+				globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
+				// Handle the global AJAX counter
+				if ( !( --jQuery.active ) ) {
+					jQuery.event.trigger("ajaxStop");
+				}
+			}
+		}
+
+		return jqXHR;
+	},
+
+	getJSON: function( url, data, callback ) {
+		return jQuery.get( url, data, callback, "json" );
+	},
+
+	getScript: function( url, callback ) {
+		return jQuery.get( url, undefined, callback, "script" );
+	}
+});
+
+jQuery.each( [ "get", "post" ], function( i, method ) {
+	jQuery[ method ] = function( url, data, callback, type ) {
+		// shift arguments if data argument was omitted
+		if ( jQuery.isFunction( data ) ) {
+			type = type || callback;
+			callback = data;
+			data = undefined;
+		}
+
+		return jQuery.ajax({
+			url: url,
+			type: method,
+			dataType: type,
+			data: data,
+			success: callback
+		});
+	};
+});
+
+// Attach a bunch of functions for handling common AJAX events
+jQuery.each( [ "ajaxStart", "ajaxStop", "ajaxComplete", "ajaxError", "ajaxSuccess", "ajaxSend" ], function( i, type ) {
+	jQuery.fn[ type ] = function( fn ) {
+		return this.on( type, fn );
+	};
+});
+
+
+jQuery._evalUrl = function( url ) {
+	return jQuery.ajax({
+		url: url,
+		type: "GET",
+		dataType: "script",
+		async: false,
+		global: false,
+		"throws": true
+	});
+};
+
+
+jQuery.fn.extend({
+	wrapAll: function( html ) {
+		if ( jQuery.isFunction( html ) ) {
+			return this.each(function(i) {
+				jQuery(this).wrapAll( html.call(this, i) );
+			});
+		}
+
+		if ( this[0] ) {
+			// The elements to wrap the target around
+			var wrap = jQuery( html, this[0].ownerDocument ).eq(0).clone(true);
+
+			if ( this[0].parentNode ) {
+				wrap.insertBefore( this[0] );
+			}
+
+			wrap.map(function() {
+				var elem = this;
+
+				while ( elem.firstChild && elem.firstChild.nodeType === 1 ) {
+					elem = elem.firstChild;
+				}
+
+				return elem;
+			}).append( this );
+		}
+
+		return this;
+	},
+
+	wrapInner: function( html ) {
+		if ( jQuery.isFunction( html ) ) {
+			return this.each(function(i) {
+				jQuery(this).wrapInner( html.call(this, i) );
+			});
+		}
+
+		return this.each(function() {
+			var self = jQuery( this ),
+				contents = self.contents();
+
+			if ( contents.length ) {
+				contents.wrapAll( html );
+
+			} else {
+				self.append( html );
+			}
+		});
+	},
+
+	wrap: function( html ) {
+		var isFunction = jQuery.isFunction( html );
+
+		return this.each(function(i) {
+			jQuery( this ).wrapAll( isFunction ? html.call(this, i) : html );
+		});
+	},
+
+	unwrap: function() {
+		return this.parent().each(function() {
+			if ( !jQuery.nodeName( this, "body" ) ) {
+				jQuery( this ).replaceWith( this.childNodes );
+			}
+		}).end();
+	}
+});
+
+
+jQuery.expr.filters.hidden = function( elem ) {
+	// Support: Opera <= 12.12
+	// Opera reports offsetWidths and offsetHeights less than zero on some elements
+	return elem.offsetWidth <= 0 && elem.offsetHeight <= 0 ||
+		(!support.reliableHiddenOffsets() &&
+			((elem.style && elem.style.display) || jQuery.css( elem, "display" )) === "none");
+};
+
+jQuery.expr.filters.visible = function( elem ) {
+	return !jQuery.expr.filters.hidden( elem );
+};
+
+
+
+
+var r20 = /%20/g,
+	rbracket = /\[\]$/,
+	rCRLF = /\r?\n/g,
+	rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
+	rsubmittable = /^(?:input|select|textarea|keygen)/i;
+
+function buildParams( prefix, obj, traditional, add ) {
+	var name;
+
+	if ( jQuery.isArray( obj ) ) {
+		// Serialize array item.
+		jQuery.each( obj, function( i, v ) {
+			if ( traditional || rbracket.test( prefix ) ) {
+				// Treat each array item as a scalar.
+				add( prefix, v );
+
+			} else {
+				// Item is non-scalar (array or object), encode its numeric index.
+				buildParams( prefix + "[" + ( typeof v === "object" ? i : "" ) + "]", v, traditional, add );
+			}
+		});
+
+	} else if ( !traditional && jQuery.type( obj ) === "object" ) {
+		// Serialize object item.
+		for ( name in obj ) {
+			buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
+		}
+
+	} else {
+		// Serialize scalar item.
+		add( prefix, obj );
+	}
+}
+
+// Serialize an array of form elements or a set of
+// key/values into a query string
+jQuery.param = function( a, traditional ) {
+	var prefix,
+		s = [],
+		add = function( key, value ) {
+			// If value is a function, invoke it and return its value
+			value = jQuery.isFunction( value ) ? value() : ( value == null ? "" : value );
+			s[ s.length ] = encodeURIComponent( key ) + "=" + encodeURIComponent( value );
+		};
+
+	// Set traditional to true for jQuery <= 1.3.2 behavior.
+	if ( traditional === undefined ) {
+		traditional = jQuery.ajaxSettings && jQuery.ajaxSettings.traditional;
+	}
+
+	// If an array was passed in, assume that it is an array of form elements.
+	if ( jQuery.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
+		// Serialize the form elements
+		jQuery.each( a, function() {
+			add( this.name, this.value );
+		});
+
+	} else {
+		// If traditional, encode the "old" way (the way 1.3.2 or older
+		// did it), otherwise encode params recursively.
+		for ( prefix in a ) {
+			buildParams( prefix, a[ prefix ], traditional, add );
+		}
+	}
+
+	// Return the resulting serialization
+	return s.join( "&" ).replace( r20, "+" );
+};
+
+jQuery.fn.extend({
+	serialize: function() {
+		return jQuery.param( this.serializeArray() );
+	},
+	serializeArray: function() {
+		return this.map(function() {
+			// Can add propHook for "elements" to filter or add form elements
+			var elements = jQuery.prop( this, "elements" );
+			return elements ? jQuery.makeArray( elements ) : this;
+		})
+		.filter(function() {
+			var type = this.type;
+			// Use .is(":disabled") so that fieldset[disabled] works
+			return this.name && !jQuery( this ).is( ":disabled" ) &&
+				rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
+				( this.checked || !rcheckableType.test( type ) );
+		})
+		.map(function( i, elem ) {
+			var val = jQuery( this ).val();
+
+			return val == null ?
+				null :
+				jQuery.isArray( val ) ?
+					jQuery.map( val, function( val ) {
+						return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+					}) :
+					{ name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+		}).get();
+	}
+});
+
+
+// Create the request object
+// (This is still attached to ajaxSettings for backward compatibility)
+jQuery.ajaxSettings.xhr = window.ActiveXObject !== undefined ?
+	// Support: IE6+
+	function() {
+
+		// XHR cannot access local files, always use ActiveX for that case
+		return !this.isLocal &&
+
+			// Support: IE7-8
+			// oldIE XHR does not support non-RFC2616 methods (#13240)
+			// See http://msdn.microsoft.com/en-us/library/ie/ms536648(v=vs.85).aspx
+			// and http://www.w3.org/Protocols/rfc2616/rfc2616-sec9.html#sec9
+			// Although this check for six methods instead of eight
+			// since IE also does not support "trace" and "connect"
+			/^(get|post|head|put|delete|options)$/i.test( this.type ) &&
+
+			createStandardXHR() || createActiveXHR();
+	} :
+	// For all other browsers, use the standard XMLHttpRequest object
+	createStandardXHR;
+
+var xhrId = 0,
+	xhrCallbacks = {},
+	xhrSupported = jQuery.ajaxSettings.xhr();
+
+// Support: IE<10
+// Open requests must be manually aborted on unload (#5280)
+if ( window.ActiveXObject ) {
+	jQuery( window ).on( "unload", function() {
+		for ( var key in xhrCallbacks ) {
+			xhrCallbacks[ key ]( undefined, true );
+		}
+	});
+}
+
+// Determine support properties
+support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
+xhrSupported = support.ajax = !!xhrSupported;
+
+// Create transport if the browser can provide an xhr
+if ( xhrSupported ) {
+
+	jQuery.ajaxTransport(function( options ) {
+		// Cross domain only allowed if supported through XMLHttpRequest
+		if ( !options.crossDomain || support.cors ) {
+
+			var callback;
+
+			return {
+				send: function( headers, complete ) {
+					var i,
+						xhr = options.xhr(),
+						id = ++xhrId;
+
+					// Open the socket
+					xhr.open( options.type, options.url, options.async, options.username, options.password );
+
+					// Apply custom fields if provided
+					if ( options.xhrFields ) {
+						for ( i in options.xhrFields ) {
+							xhr[ i ] = options.xhrFields[ i ];
+						}
+					}
+
+					// Override mime type if needed
+					if ( options.mimeType && xhr.overrideMimeType ) {
+						xhr.overrideMimeType( options.mimeType );
+					}
+
+					// X-Requested-With header
+					// For cross-domain requests, seeing as conditions for a preflight are
+					// akin to a jigsaw puzzle, we simply never set it to be sure.
+					// (it can always be set on a per-request basis or even using ajaxSetup)
+					// For same-domain requests, won't change header if already provided.
+					if ( !options.crossDomain && !headers["X-Requested-With"] ) {
+						headers["X-Requested-With"] = "XMLHttpRequest";
+					}
+
+					// Set headers
+					for ( i in headers ) {
+						// Support: IE<9
+						// IE's ActiveXObject throws a 'Type Mismatch' exception when setting
+						// request header to a null-value.
+						//
+						// To keep consistent with other XHR implementations, cast the value
+						// to string and ignore `undefined`.
+						if ( headers[ i ] !== undefined ) {
+							xhr.setRequestHeader( i, headers[ i ] + "" );
+						}
+					}
+
+					// Do send the request
+					// This may raise an exception which is actually
+					// handled in jQuery.ajax (so no try/catch here)
+					xhr.send( ( options.hasContent && options.data ) || null );
+
+					// Listener
+					callback = function( _, isAbort ) {
+						var status, statusText, responses;
+
+						// Was never called and is aborted or complete
+						if ( callback && ( isAbort || xhr.readyState === 4 ) ) {
+							// Clean up
+							delete xhrCallbacks[ id ];
+							callback = undefined;
+							xhr.onreadystatechange = jQuery.noop;
+
+							// Abort manually if needed
+							if ( isAbort ) {
+								if ( xhr.readyState !== 4 ) {
+									xhr.abort();
+								}
+							} else {
+								responses = {};
+								status = xhr.status;
+
+								// Support: IE<10
+								// Accessing binary-data responseText throws an exception
+								// (#11426)
+								if ( typeof xhr.responseText === "string" ) {
+									responses.text = xhr.responseText;
+								}
+
+								// Firefox throws an exception when accessing
+								// statusText for faulty cross-domain requests
+								try {
+									statusText = xhr.statusText;
+								} catch( e ) {
+									// We normalize with Webkit giving an empty statusText
+									statusText = "";
+								}
+
+								// Filter status for non standard behaviors
+
+								// If the request is local and we have data: assume a success
+								// (success with no data won't get notified, that's the best we
+								// can do given current implementations)
+								if ( !status && options.isLocal && !options.crossDomain ) {
+									status = responses.text ? 200 : 404;
+								// IE - #1450: sometimes returns 1223 when it should be 204
+								} else if ( status === 1223 ) {
+									status = 204;
+								}
+							}
+						}
+
+						// Call complete if needed
+						if ( responses ) {
+							complete( status, statusText, responses, xhr.getAllResponseHeaders() );
+						}
+					};
+
+					if ( !options.async ) {
+						// if we're in sync mode we fire the callback
+						callback();
+					} else if ( xhr.readyState === 4 ) {
+						// (IE6 & IE7) if it's in cache and has been
+						// retrieved directly we need to fire the callback
+						setTimeout( callback );
+					} else {
+						// Add to the list of active xhr callbacks
+						xhr.onreadystatechange = xhrCallbacks[ id ] = callback;
+					}
+				},
+
+				abort: function() {
+					if ( callback ) {
+						callback( undefined, true );
+					}
+				}
+			};
+		}
+	});
+}
+
+// Functions to create xhrs
+function createStandardXHR() {
+	try {
+		return new window.XMLHttpRequest();
+	} catch( e ) {}
+}
+
+function createActiveXHR() {
+	try {
+		return new window.ActiveXObject( "Microsoft.XMLHTTP" );
+	} catch( e ) {}
+}
+
+
+
+
+// Install script dataType
+jQuery.ajaxSetup({
+	accepts: {
+		script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"
+	},
+	contents: {
+		script: /(?:java|ecma)script/
+	},
+	converters: {
+		"text script": function( text ) {
+			jQuery.globalEval( text );
+			return text;
+		}
+	}
+});
+
+// Handle cache's special case and global
+jQuery.ajaxPrefilter( "script", function( s ) {
+	if ( s.cache === undefined ) {
+		s.cache = false;
+	}
+	if ( s.crossDomain ) {
+		s.type = "GET";
+		s.global = false;
+	}
+});
+
+// Bind script tag hack transport
+jQuery.ajaxTransport( "script", function(s) {
+
+	// This transport only deals with cross domain requests
+	if ( s.crossDomain ) {
+
+		var script,
+			head = document.head || jQuery("head")[0] || document.documentElement;
+
+		return {
+
+			send: function( _, callback ) {
+
+				script = document.createElement("script");
+
+				script.async = true;
+
+				if ( s.scriptCharset ) {
+					script.charset = s.scriptCharset;
+				}
+
+				script.src = s.url;
+
+				// Attach handlers for all browsers
+				script.onload = script.onreadystatechange = function( _, isAbort ) {
+
+					if ( isAbort || !script.readyState || /loaded|complete/.test( script.readyState ) ) {
+
+						// Handle memory leak in IE
+						script.onload = script.onreadystatechange = null;
+
+						// Remove the script
+						if ( script.parentNode ) {
+							script.parentNode.removeChild( script );
+						}
+
+						// Dereference the script
+						script = null;
+
+						// Callback if not abort
+						if ( !isAbort ) {
+							callback( 200, "success" );
+						}
+					}
+				};
+
+				// Circumvent IE6 bugs with base elements (#2709 and #4378) by prepending
+				// Use native DOM manipulation to avoid our domManip AJAX trickery
+				head.insertBefore( script, head.firstChild );
+			},
+
+			abort: function() {
+				if ( script ) {
+					script.onload( undefined, true );
+				}
+			}
+		};
+	}
+});
+
+
+
+
+var oldCallbacks = [],
+	rjsonp = /(=)\?(?=&|$)|\?\?/;
+
+// Default jsonp settings
+jQuery.ajaxSetup({
+	jsonp: "callback",
+	jsonpCallback: function() {
+		var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce++ ) );
+		this[ callback ] = true;
+		return callback;
+	}
+});
+
+// Detect, normalize options and install callbacks for jsonp requests
+jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
+
+	var callbackName, overwritten, responseContainer,
+		jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ?
+			"url" :
+			typeof s.data === "string" && !( s.contentType || "" ).indexOf("application/x-www-form-urlencoded") && rjsonp.test( s.data ) && "data"
+		);
+
+	// Handle iff the expected data type is "jsonp" or we have a parameter to set
+	if ( jsonProp || s.dataTypes[ 0 ] === "jsonp" ) {
+
+		// Get callback name, remembering preexisting value associated with it
+		callbackName = s.jsonpCallback = jQuery.isFunction( s.jsonpCallback ) ?
+			s.jsonpCallback() :
+			s.jsonpCallback;
+
+		// Insert callback into url or form data
+		if ( jsonProp ) {
+			s[ jsonProp ] = s[ jsonProp ].replace( rjsonp, "$1" + callbackName );
+		} else if ( s.jsonp !== false ) {
+			s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName;
+		}
+
+		// Use data converter to retrieve json after script execution
+		s.converters["script json"] = function() {
+			if ( !responseContainer ) {
+				jQuery.error( callbackName + " was not called" );
+			}
+			return responseContainer[ 0 ];
+		};
+
+		// force json dataType
+		s.dataTypes[ 0 ] = "json";
+
+		// Install callback
+		overwritten = window[ callbackName ];
+		window[ callbackName ] = function() {
+			responseContainer = arguments;
+		};
+
+		// Clean-up function (fires after converters)
+		jqXHR.always(function() {
+			// Restore preexisting value
+			window[ callbackName ] = overwritten;
+
+			// Save back as free
+			if ( s[ callbackName ] ) {
+				// make sure that re-using the options doesn't screw things around
+				s.jsonpCallback = originalSettings.jsonpCallback;
+
+				// save the callback name for future use
+				oldCallbacks.push( callbackName );
+			}
+
+			// Call if it was a function and we have a response
+			if ( responseContainer && jQuery.isFunction( overwritten ) ) {
+				overwritten( responseContainer[ 0 ] );
+			}
+
+			responseContainer = overwritten = undefined;
+		});
+
+		// Delegate to script
+		return "script";
+	}
+});
+
+
+
+
+// data: string of html
+// context (optional): If specified, the fragment will be created in this context, defaults to document
+// keepScripts (optional): If true, will include scripts passed in the html string
+jQuery.parseHTML = function( data, context, keepScripts ) {
+	if ( !data || typeof data !== "string" ) {
+		return null;
+	}
+	if ( typeof context === "boolean" ) {
+		keepScripts = context;
+		context = false;
+	}
+	context = context || document;
+
+	var parsed = rsingleTag.exec( data ),
+		scripts = !keepScripts && [];
+
+	// Single tag
+	if ( parsed ) {
+		return [ context.createElement( parsed[1] ) ];
+	}
+
+	parsed = jQuery.buildFragment( [ data ], context, scripts );
+
+	if ( scripts && scripts.length ) {
+		jQuery( scripts ).remove();
+	}
+
+	return jQuery.merge( [], parsed.childNodes );
+};
+
+
+// Keep a copy of the old load method
+var _load = jQuery.fn.load;
+
+/**
+ * Load a url into a page
+ */
+jQuery.fn.load = function( url, params, callback ) {
+	if ( typeof url !== "string" && _load ) {
+		return _load.apply( this, arguments );
+	}
+
+	var selector, response, type,
+		self = this,
+		off = url.indexOf(" ");
+
+	if ( off >= 0 ) {
+		selector = jQuery.trim( url.slice( off, url.length ) );
+		url = url.slice( 0, off );
+	}
+
+	// If it's a function
+	if ( jQuery.isFunction( params ) ) {
+
+		// We assume that it's the callback
+		callback = params;
+		params = undefined;
+
+	// Otherwise, build a param string
+	} else if ( params && typeof params === "object" ) {
+		type = "POST";
+	}
+
+	// If we have elements to modify, make the request
+	if ( self.length > 0 ) {
+		jQuery.ajax({
+			url: url,
+
+			// if "type" variable is undefined, then "GET" method will be used
+			type: type,
+			dataType: "html",
+			data: params
+		}).done(function( responseText ) {
+
+			// Save response for use in complete callback
+			response = arguments;
+
+			self.html( selector ?
+
+				// If a selector was specified, locate the right elements in a dummy div
+				// Exclude scripts to avoid IE 'Permission Denied' errors
+				jQuery("<div>").append( jQuery.parseHTML( responseText ) ).find( selector ) :
+
+				// Otherwise use the full result
+				responseText );
+
+		}).complete( callback && function( jqXHR, status ) {
+			self.each( callback, response || [ jqXHR.responseText, status, jqXHR ] );
+		});
+	}
+
+	return this;
+};
+
+
+
+
+jQuery.expr.filters.animated = function( elem ) {
+	return jQuery.grep(jQuery.timers, function( fn ) {
+		return elem === fn.elem;
+	}).length;
+};
+
+
+
+
+
+var docElem = window.document.documentElement;
+
+/**
+ * Gets a window from an element
+ */
+function getWindow( elem ) {
+	return jQuery.isWindow( elem ) ?
+		elem :
+		elem.nodeType === 9 ?
+			elem.defaultView || elem.parentWindow :
+			false;
+}
+
+jQuery.offset = {
+	setOffset: function( elem, options, i ) {
+		var curPosition, curLeft, curCSSTop, curTop, curOffset, curCSSLeft, calculatePosition,
+			position = jQuery.css( elem, "position" ),
+			curElem = jQuery( elem ),
+			props = {};
+
+		// set position first, in-case top/left are set even on static elem
+		if ( position === "static" ) {
+			elem.style.position = "relative";
+		}
+
+		curOffset = curElem.offset();
+		curCSSTop = jQuery.css( elem, "top" );
+		curCSSLeft = jQuery.css( elem, "left" );
+		calculatePosition = ( position === "absolute" || position === "fixed" ) &&
+			jQuery.inArray("auto", [ curCSSTop, curCSSLeft ] ) > -1;
+
+		// need to be able to calculate position if either top or left is auto and position is either absolute or fixed
+		if ( calculatePosition ) {
+			curPosition = curElem.position();
+			curTop = curPosition.top;
+			curLeft = curPosition.left;
+		} else {
+			curTop = parseFloat( curCSSTop ) || 0;
+			curLeft = parseFloat( curCSSLeft ) || 0;
+		}
+
+		if ( jQuery.isFunction( options ) ) {
+			options = options.call( elem, i, curOffset );
+		}
+
+		if ( options.top != null ) {
+			props.top = ( options.top - curOffset.top ) + curTop;
+		}
+		if ( options.left != null ) {
+			props.left = ( options.left - curOffset.left ) + curLeft;
+		}
+
+		if ( "using" in options ) {
+			options.using.call( elem, props );
+		} else {
+			curElem.css( props );
+		}
+	}
+};
+
+jQuery.fn.extend({
+	offset: function( options ) {
+		if ( arguments.length ) {
+			return options === undefined ?
+				this :
+				this.each(function( i ) {
+					jQuery.offset.setOffset( this, options, i );
+				});
+		}
+
+		var docElem, win,
+			box = { top: 0, left: 0 },
+			elem = this[ 0 ],
+			doc = elem && elem.ownerDocument;
+
+		if ( !doc ) {
+			return;
+		}
+
+		docElem = doc.documentElement;
+
+		// Make sure it's not a disconnected DOM node
+		if ( !jQuery.contains( docElem, elem ) ) {
+			return box;
+		}
+
+		// If we don't have gBCR, just use 0,0 rather than error
+		// BlackBerry 5, iOS 3 (original iPhone)
+		if ( typeof elem.getBoundingClientRect !== strundefined ) {
+			box = elem.getBoundingClientRect();
+		}
+		win = getWindow( doc );
+		return {
+			top: box.top  + ( win.pageYOffset || docElem.scrollTop )  - ( docElem.clientTop  || 0 ),
+			left: box.left + ( win.pageXOffset || docElem.scrollLeft ) - ( docElem.clientLeft || 0 )
+		};
+	},
+
+	position: function() {
+		if ( !this[ 0 ] ) {
+			return;
+		}
+
+		var offsetParent, offset,
+			parentOffset = { top: 0, left: 0 },
+			elem = this[ 0 ];
+
+		// fixed elements are offset from window (parentOffset = {top:0, left: 0}, because it is its only offset parent
+		if ( jQuery.css( elem, "position" ) === "fixed" ) {
+			// we assume that getBoundingClientRect is available when computed position is fixed
+			offset = elem.getBoundingClientRect();
+		} else {
+			// Get *real* offsetParent
+			offsetParent = this.offsetParent();
+
+			// Get correct offsets
+			offset = this.offset();
+			if ( !jQuery.nodeName( offsetParent[ 0 ], "html" ) ) {
+				parentOffset = offsetParent.offset();
+			}
+
+			// Add offsetParent borders
+			parentOffset.top  += jQuery.css( offsetParent[ 0 ], "borderTopWidth", true );
+			parentOffset.left += jQuery.css( offsetParent[ 0 ], "borderLeftWidth", true );
+		}
+
+		// Subtract parent offsets and element margins
+		// note: when an element has margin: auto the offsetLeft and marginLeft
+		// are the same in Safari causing offset.left to incorrectly be 0
+		return {
+			top:  offset.top  - parentOffset.top - jQuery.css( elem, "marginTop", true ),
+			left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true)
+		};
+	},
+
+	offsetParent: function() {
+		return this.map(function() {
+			var offsetParent = this.offsetParent || docElem;
+
+			while ( offsetParent && ( !jQuery.nodeName( offsetParent, "html" ) && jQuery.css( offsetParent, "position" ) === "static" ) ) {
+				offsetParent = offsetParent.offsetParent;
+			}
+			return offsetParent || docElem;
+		});
+	}
+});
+
+// Create scrollLeft and scrollTop methods
+jQuery.each( { scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function( method, prop ) {
+	var top = /Y/.test( prop );
+
+	jQuery.fn[ method ] = function( val ) {
+		return access( this, function( elem, method, val ) {
+			var win = getWindow( elem );
+
+			if ( val === undefined ) {
+				return win ? (prop in win) ? win[ prop ] :
+					win.document.documentElement[ method ] :
+					elem[ method ];
+			}
+
+			if ( win ) {
+				win.scrollTo(
+					!top ? val : jQuery( win ).scrollLeft(),
+					top ? val : jQuery( win ).scrollTop()
+				);
+
+			} else {
+				elem[ method ] = val;
+			}
+		}, method, val, arguments.length, null );
+	};
+});
+
+// Add the top/left cssHooks using jQuery.fn.position
+// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084
+// getComputedStyle returns percent when specified for top/left/bottom/right
+// rather than make the css module depend on the offset module, we just check for it here
+jQuery.each( [ "top", "left" ], function( i, prop ) {
+	jQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition,
+		function( elem, computed ) {
+			if ( computed ) {
+				computed = curCSS( elem, prop );
+				// if curCSS returns percentage, fallback to offset
+				return rnumnonpx.test( computed ) ?
+					jQuery( elem ).position()[ prop ] + "px" :
+					computed;
+			}
+		}
+	);
+});
+
+
+// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods
+jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
+	jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name }, function( defaultExtra, funcName ) {
+		// margin is only for outerHeight, outerWidth
+		jQuery.fn[ funcName ] = function( margin, value ) {
+			var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ),
+				extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" );
+
+			return access( this, function( elem, type, value ) {
+				var doc;
+
+				if ( jQuery.isWindow( elem ) ) {
+					// As of 5/8/2012 this will yield incorrect results for Mobile Safari, but there
+					// isn't a whole lot we can do. See pull request at this URL for discussion:
+					// https://github.com/jquery/jquery/pull/764
+					return elem.document.documentElement[ "client" + name ];
+				}
+
+				// Get document width or height
+				if ( elem.nodeType === 9 ) {
+					doc = elem.documentElement;
+
+					// Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height], whichever is greatest
+					// unfortunately, this causes bug #3838 in IE6/8 only, but there is currently no good, small way to fix it.
+					return Math.max(
+						elem.body[ "scroll" + name ], doc[ "scroll" + name ],
+						elem.body[ "offset" + name ], doc[ "offset" + name ],
+						doc[ "client" + name ]
+					);
+				}
+
+				return value === undefined ?
+					// Get width or height on the element, requesting but not forcing parseFloat
+					jQuery.css( elem, type, extra ) :
+
+					// Set width or height on the element
+					jQuery.style( elem, type, value, extra );
+			}, type, chainable ? margin : undefined, chainable, null );
+		};
+	});
+});
+
+
+// The number of elements contained in the matched element set
+jQuery.fn.size = function() {
+	return this.length;
+};
+
+jQuery.fn.andSelf = jQuery.fn.addBack;
+
+
+
+
+// Register as a named AMD module, since jQuery can be concatenated with other
+// files that may use define, but not via a proper concatenation script that
+// understands anonymous AMD modules. A named AMD is safest and most robust
+// way to register. Lowercase jquery is used because AMD module names are
+// derived from file names, and jQuery is normally delivered in a lowercase
+// file name. Do this after creating the global so that if an AMD module wants
+// to call noConflict to hide this version of jQuery, it will work.
+
+// Note that for maximum portability, libraries that are not jQuery should
+// declare themselves as anonymous modules, and avoid setting a global if an
+// AMD loader is present. jQuery is a special case. For more information, see
+// https://github.com/jrburke/requirejs/wiki/Updating-existing-libraries#wiki-anon
+
+if ( typeof define === "function" && define.amd ) {
+	define( "jquery", [], function() {
+		return jQuery;
+	});
+}
+
+
+
+
+var
+	// Map over jQuery in case of overwrite
+	_jQuery = window.jQuery,
+
+	// Map over the $ in case of overwrite
+	_$ = window.$;
+
+jQuery.noConflict = function( deep ) {
+	if ( window.$ === jQuery ) {
+		window.$ = _$;
+	}
+
+	if ( deep && window.jQuery === jQuery ) {
+		window.jQuery = _jQuery;
+	}
+
+	return jQuery;
+};
+
+// Expose jQuery and $ identifiers, even in
+// AMD (#7102#comment:10, https://github.com/jquery/jquery/pull/557)
+// and CommonJS for browser emulators (#13566)
+if ( typeof noGlobal === strundefined ) {
+	window.jQuery = window.$ = jQuery;
+}
+
+
+
+
+return jQuery;
+
+}));
diff --git a/package/doc/html/_static/jquery.js b/package/doc/html/_static/jquery.js
index 7c243080233..ab28a24729b 100644
--- a/package/doc/html/_static/jquery.js
+++ b/package/doc/html/_static/jquery.js
@@ -1,154 +1,4 @@
-/*!
- * jQuery JavaScript Library v1.4.2
- * http://jquery.com/
- *
- * Copyright 2010, John Resig
- * Dual licensed under the MIT or GPL Version 2 licenses.
- * http://jquery.org/license
- *
- * Includes Sizzle.js
- * http://sizzlejs.com/
- * Copyright 2010, The Dojo Foundation
- * Released under the MIT, BSD, and GPL Licenses.
- *
- * Date: Sat Feb 13 22:33:48 2010 -0500
- */
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diff --git a/package/doc/html/_static/minus.png b/package/doc/html/_static/minus.png
index da1c5620d10..0f22b16b038 100644
Binary files a/package/doc/html/_static/minus.png and b/package/doc/html/_static/minus.png differ
diff --git a/package/doc/html/_static/opensearch.xml b/package/doc/html/_static/opensearch.xml
index 82fec85a26d..7500794b454 100644
--- a/package/doc/html/_static/opensearch.xml
+++ b/package/doc/html/_static/opensearch.xml
@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <OpenSearchDescription xmlns="http://a9.com/-/spec/opensearch/1.1/">
   <ShortName>MDAnalysis</ShortName>
-  <Description>Search MDAnalysis 0.11.0-dev documentation</Description>
+  <Description>Search MDAnalysis 0.11.0 documentation</Description>
   <InputEncoding>utf-8</InputEncoding>
   <Url type="text/html" method="get"
        template="http://pythonhosted.org/MDAnalysis/search.html?q={searchTerms}&amp;check_keywords=yes&amp;area=default"/>
-  <LongName>MDAnalysis 0.11.0-dev documentation</LongName>
+  <LongName>MDAnalysis 0.11.0 documentation</LongName>
   
 </OpenSearchDescription>
\ No newline at end of file
diff --git a/package/doc/html/_static/plus.png b/package/doc/html/_static/plus.png
index b3cb37425ea..0cfe084cfc8 100644
Binary files a/package/doc/html/_static/plus.png and b/package/doc/html/_static/plus.png differ
diff --git a/package/doc/html/_static/pygments.css b/package/doc/html/_static/pygments.css
index d79caa151c2..57eadc030ea 100644
--- a/package/doc/html/_static/pygments.css
+++ b/package/doc/html/_static/pygments.css
@@ -40,6 +40,7 @@
 .highlight .nv { color: #bb60d5 } /* Name.Variable */
 .highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
 .highlight .w { color: #bbbbbb } /* Text.Whitespace */
+.highlight .mb { color: #208050 } /* Literal.Number.Bin */
 .highlight .mf { color: #208050 } /* Literal.Number.Float */
 .highlight .mh { color: #208050 } /* Literal.Number.Hex */
 .highlight .mi { color: #208050 } /* Literal.Number.Integer */
diff --git a/package/doc/html/_static/searchtools.js b/package/doc/html/_static/searchtools.js
index 663be4c909b..0e794fd3e90 100644
--- a/package/doc/html/_static/searchtools.js
+++ b/package/doc/html/_static/searchtools.js
@@ -4,38 +4,11 @@
  *
  * Sphinx JavaScript utilties for the full-text search.
  *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
-/**
- * helper function to return a node containing the
- * search summary for a given text. keywords is a list
- * of stemmed words, hlwords is the list of normal, unstemmed
- * words. the first one is used to find the occurance, the
- * latter for highlighting it.
- */
-
-jQuery.makeSearchSummary = function(text, keywords, hlwords) {
-  var textLower = text.toLowerCase();
-  var start = 0;
-  $.each(keywords, function() {
-    var i = textLower.indexOf(this.toLowerCase());
-    if (i > -1)
-      start = i;
-  });
-  start = Math.max(start - 120, 0);
-  var excerpt = ((start > 0) ? '...' : '') +
-  $.trim(text.substr(start, 240)) +
-  ((start + 240 - text.length) ? '...' : '');
-  var rv = $('<div class="context"></div>').text(excerpt);
-  $.each(hlwords, function() {
-    rv = rv.highlightText(this, 'highlighted');
-  });
-  return rv;
-}
-
 
 /**
  * Porter Stemmer
@@ -220,6 +193,38 @@ var Stemmer = function() {
 }
 
 
+
+/**
+ * Simple result scoring code.
+ */
+var Scorer = {
+  // Implement the following function to further tweak the score for each result
+  // The function takes a result array [filename, title, anchor, descr, score]
+  // and returns the new score.
+  /*
+  score: function(result) {
+    return result[4];
+  },
+  */
+
+  // query matches the full name of an object
+  objNameMatch: 11,
+  // or matches in the last dotted part of the object name
+  objPartialMatch: 6,
+  // Additive scores depending on the priority of the object
+  objPrio: {0:  15,   // used to be importantResults
+            1:  5,   // used to be objectResults
+            2: -5},  // used to be unimportantResults
+  //  Used when the priority is not in the mapping.
+  objPrioDefault: 0,
+
+  // query found in title
+  title: 15,
+  // query found in terms
+  term: 5
+};
+
+
 /**
  * Search Module
  */
@@ -239,8 +244,13 @@ var Search = {
   },
 
   loadIndex : function(url) {
-    $.ajax({type: "GET", url: url, data: null, success: null,
-            dataType: "script", cache: true});
+    $.ajax({type: "GET", url: url, data: null,
+            dataType: "script", cache: true,
+            complete: function(jqxhr, textstatus) {
+              if (textstatus != "success") {
+                document.getElementById("searchindexloader").src = url;
+              }
+            }});
   },
 
   setIndex : function(index) {
@@ -268,19 +278,20 @@ var Search = {
     if (this._pulse_status >= 0)
         return;
     function pulse() {
+      var i;
       Search._pulse_status = (Search._pulse_status + 1) % 4;
       var dotString = '';
-      for (var i = 0; i < Search._pulse_status; i++)
+      for (i = 0; i < Search._pulse_status; i++)
         dotString += '.';
       Search.dots.text(dotString);
       if (Search._pulse_status > -1)
         window.setTimeout(pulse, 500);
-    };
+    }
     pulse();
   },
 
   /**
-   * perform a search for something
+   * perform a search for something (or wait until index is loaded)
    */
   performSearch : function(query) {
     // create the required interface elements
@@ -300,41 +311,46 @@ var Search = {
       this.deferQuery(query);
   },
 
+  /**
+   * execute search (requires search index to be loaded)
+   */
   query : function(query) {
-    var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
+    var i;
+    var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
 
-    // Stem the searchterms and add them to the correct list
+    // stem the searchterms and add them to the correct list
     var stemmer = new Stemmer();
     var searchterms = [];
     var excluded = [];
     var hlterms = [];
     var tmp = query.split(/\s+/);
     var objectterms = [];
-    for (var i = 0; i < tmp.length; i++) {
-      if (tmp[i] != "") {
+    for (i = 0; i < tmp.length; i++) {
+      if (tmp[i] !== "") {
           objectterms.push(tmp[i].toLowerCase());
       }
 
-      if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
-          tmp[i] == "") {
+      if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
+          tmp[i] === "") {
         // skip this "word"
         continue;
       }
       // stem the word
-      var word = stemmer.stemWord(tmp[i]).toLowerCase();
+      var word = stemmer.stemWord(tmp[i].toLowerCase());
+      var toAppend;
       // select the correct list
       if (word[0] == '-') {
-        var toAppend = excluded;
+        toAppend = excluded;
         word = word.substr(1);
       }
       else {
-        var toAppend = searchterms;
+        toAppend = searchterms;
         hlterms.push(tmp[i].toLowerCase());
       }
       // only add if not already in the list
-      if (!$.contains(toAppend, word))
+      if (!$u.contains(toAppend, word))
         toAppend.push(word);
-    };
+    }
     var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
 
     // console.debug('SEARCH: searching for:');
@@ -342,89 +358,51 @@ var Search = {
     // console.info('excluded: ', excluded);
 
     // prepare search
-    var filenames = this._index.filenames;
-    var titles = this._index.titles;
     var terms = this._index.terms;
-    var fileMap = {};
-    var files = null;
-    // different result priorities
-    var importantResults = [];
-    var objectResults = [];
-    var regularResults = [];
-    var unimportantResults = [];
+    var titleterms = this._index.titleterms;
+
+    // array of [filename, title, anchor, descr, score]
+    var results = [];
     $('#search-progress').empty();
 
     // lookup as object
-    for (var i = 0; i < objectterms.length; i++) {
-      var others = [].concat(objectterms.slice(0,i),
-                             objectterms.slice(i+1, objectterms.length))
-      var results = this.performObjectSearch(objectterms[i], others);
-      // Assume first word is most likely to be the object,
-      // other words more likely to be in description.
-      // Therefore put matches for earlier words first.
-      // (Results are eventually used in reverse order).
-      objectResults = results[0].concat(objectResults);
-      importantResults = results[1].concat(importantResults);
-      unimportantResults = results[2].concat(unimportantResults);
+    for (i = 0; i < objectterms.length; i++) {
+      var others = [].concat(objectterms.slice(0, i),
+                             objectterms.slice(i+1, objectterms.length));
+      results = results.concat(this.performObjectSearch(objectterms[i], others));
     }
 
-    // perform the search on the required terms
-    for (var i = 0; i < searchterms.length; i++) {
-      var word = searchterms[i];
-      // no match but word was a required one
-      if ((files = terms[word]) == null)
-        break;
-      if (files.length == undefined) {
-        files = [files];
-      }
-      // create the mapping
-      for (var j = 0; j < files.length; j++) {
-        var file = files[j];
-        if (file in fileMap)
-          fileMap[file].push(word);
-        else
-          fileMap[file] = [word];
-      }
-    }
-
-    // now check if the files don't contain excluded terms
-    for (var file in fileMap) {
-      var valid = true;
-
-      // check if all requirements are matched
-      if (fileMap[file].length != searchterms.length)
-        continue;
-
-      // ensure that none of the excluded terms is in the
-      // search result.
-      for (var i = 0; i < excluded.length; i++) {
-        if (terms[excluded[i]] == file ||
-            $.contains(terms[excluded[i]] || [], file)) {
-          valid = false;
-          break;
-        }
-      }
+    // lookup as search terms in fulltext
+    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term))
+                     .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title));
 
-      // if we have still a valid result we can add it
-      // to the result list
-      if (valid)
-        regularResults.push([filenames[file], titles[file], '', null]);
+    // let the scorer override scores with a custom scoring function
+    if (Scorer.score) {
+      for (i = 0; i < results.length; i++)
+        results[i][4] = Scorer.score(results[i]);
     }
 
-    // delete unused variables in order to not waste
-    // memory until list is retrieved completely
-    delete filenames, titles, terms;
-
-    // now sort the regular results descending by title
-    regularResults.sort(function(a, b) {
-      var left = a[1].toLowerCase();
-      var right = b[1].toLowerCase();
-      return (left > right) ? -1 : ((left < right) ? 1 : 0);
+    // now sort the results by score (in opposite order of appearance, since the
+    // display function below uses pop() to retrieve items) and then
+    // alphabetically
+    results.sort(function(a, b) {
+      var left = a[4];
+      var right = b[4];
+      if (left > right) {
+        return 1;
+      } else if (left < right) {
+        return -1;
+      } else {
+        // same score: sort alphabetically
+        left = a[1].toLowerCase();
+        right = b[1].toLowerCase();
+        return (left > right) ? -1 : ((left < right) ? 1 : 0);
+      }
     });
 
-    // combine all results
-    var results = unimportantResults.concat(regularResults)
-      .concat(objectResults).concat(importantResults);
+    // for debugging
+    //Search.lastresults = results.slice();  // a copy
+    //console.info('search results:', Search.lastresults);
 
     // print the results
     var resultCount = results.length;
@@ -433,7 +411,7 @@ var Search = {
       if (results.length) {
         var item = results.pop();
         var listItem = $('<li style="display:none"></li>');
-        if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') {
+        if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') {
           // dirhtml builder
           var dirname = item[0] + '/';
           if (dirname.match(/\/index\/$/)) {
@@ -457,16 +435,18 @@ var Search = {
             displayNextItem();
           });
         } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
-          $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' +
-                item[0] + '.txt', function(data) {
-            if (data != '') {
-              listItem.append($.makeSearchSummary(data, searchterms, hlterms));
-              Search.output.append(listItem);
-            }
-            listItem.slideDown(5, function() {
-              displayNextItem();
-            });
-          }, "text");
+          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt',
+                  dataType: "text",
+                  complete: function(jqxhr, textstatus) {
+                    var data = jqxhr.responseText;
+                    if (data !== '' && data !== undefined) {
+                      listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
+                    }
+                    Search.output.append(listItem);
+                    listItem.slideDown(5, function() {
+                      displayNextItem();
+                    });
+                  }});
         } else {
           // no source available, just display title
           Search.output.append(listItem);
@@ -489,20 +469,32 @@ var Search = {
     displayNextItem();
   },
 
+  /**
+   * search for object names
+   */
   performObjectSearch : function(object, otherterms) {
     var filenames = this._index.filenames;
     var objects = this._index.objects;
     var objnames = this._index.objnames;
     var titles = this._index.titles;
 
-    var importantResults = [];
-    var objectResults = [];
-    var unimportantResults = [];
+    var i;
+    var results = [];
 
     for (var prefix in objects) {
       for (var name in objects[prefix]) {
         var fullname = (prefix ? prefix + '.' : '') + name;
         if (fullname.toLowerCase().indexOf(object) > -1) {
+          var score = 0;
+          var parts = fullname.split('.');
+          // check for different match types: exact matches of full name or
+          // "last name" (i.e. last dotted part)
+          if (fullname == object || parts[parts.length - 1] == object) {
+            score += Scorer.objNameMatch;
+          // matches in last name
+          } else if (parts[parts.length - 1].indexOf(object) > -1) {
+            score += Scorer.objPartialMatch;
+          }
           var match = objects[prefix][name];
           var objname = objnames[match[1]][2];
           var title = titles[match[0]];
@@ -512,7 +504,7 @@ var Search = {
             var haystack = (prefix + ' ' + name + ' ' +
                             objname + ' ' + title).toLowerCase();
             var allfound = true;
-            for (var i = 0; i < otherterms.length; i++) {
+            for (i = 0; i < otherterms.length; i++) {
               if (haystack.indexOf(otherterms[i]) == -1) {
                 allfound = false;
                 break;
@@ -523,37 +515,107 @@ var Search = {
             }
           }
           var descr = objname + _(', in ') + title;
-          anchor = match[3];
-          if (anchor == '')
+
+          var anchor = match[3];
+          if (anchor === '')
             anchor = fullname;
           else if (anchor == '-')
             anchor = objnames[match[1]][1] + '-' + fullname;
-          result = [filenames[match[0]], fullname, '#'+anchor, descr];
-          switch (match[2]) {
-          case 1: objectResults.push(result); break;
-          case 0: importantResults.push(result); break;
-          case 2: unimportantResults.push(result); break;
+          // add custom score for some objects according to scorer
+          if (Scorer.objPrio.hasOwnProperty(match[2])) {
+            score += Scorer.objPrio[match[2]];
+          } else {
+            score += Scorer.objPrioDefault;
           }
+          results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]);
         }
       }
     }
 
-    // sort results descending
-    objectResults.sort(function(a, b) {
-      return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
-    });
+    return results;
+  },
 
-    importantResults.sort(function(a, b) {
-      return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
-    });
+  /**
+   * search for full-text terms in the index
+   */
+  performTermsSearch : function(searchterms, excluded, terms, score) {
+    var filenames = this._index.filenames;
+    var titles = this._index.titles;
 
-    unimportantResults.sort(function(a, b) {
-      return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
-    });
+    var i, j, file, files;
+    var fileMap = {};
+    var results = [];
+
+    // perform the search on the required terms
+    for (i = 0; i < searchterms.length; i++) {
+      var word = searchterms[i];
+      // no match but word was a required one
+      if ((files = terms[word]) === undefined)
+        break;
+      if (files.length === undefined) {
+        files = [files];
+      }
+      // create the mapping
+      for (j = 0; j < files.length; j++) {
+        file = files[j];
+        if (file in fileMap)
+          fileMap[file].push(word);
+        else
+          fileMap[file] = [word];
+      }
+    }
+
+    // now check if the files don't contain excluded terms
+    for (file in fileMap) {
+      var valid = true;
+
+      // check if all requirements are matched
+      if (fileMap[file].length != searchterms.length)
+          continue;
+
+      // ensure that none of the excluded terms is in the search result
+      for (i = 0; i < excluded.length; i++) {
+        if (terms[excluded[i]] == file ||
+          $u.contains(terms[excluded[i]] || [], file)) {
+          valid = false;
+          break;
+        }
+      }
+
+      // if we have still a valid result we can add it to the result list
+      if (valid) {
+        results.push([filenames[file], titles[file], '', null, score]);
+      }
+    }
+    return results;
+  },
 
-    return [importantResults, objectResults, unimportantResults]
+  /**
+   * helper function to return a node containing the
+   * search summary for a given text. keywords is a list
+   * of stemmed words, hlwords is the list of normal, unstemmed
+   * words. the first one is used to find the occurance, the
+   * latter for highlighting it.
+   */
+  makeSearchSummary : function(text, keywords, hlwords) {
+    var textLower = text.toLowerCase();
+    var start = 0;
+    $.each(keywords, function() {
+      var i = textLower.indexOf(this.toLowerCase());
+      if (i > -1)
+        start = i;
+    });
+    start = Math.max(start - 120, 0);
+    var excerpt = ((start > 0) ? '...' : '') +
+      $.trim(text.substr(start, 240)) +
+      ((start + 240 - text.length) ? '...' : '');
+    var rv = $('<div class="context"></div>').text(excerpt);
+    $.each(hlwords, function() {
+      rv = rv.highlightText(this, 'highlighted');
+    });
+    return rv;
   }
-}
+};
 
 $(document).ready(function() {
   Search.init();
diff --git a/package/doc/html/_static/sphinxdoc.css b/package/doc/html/_static/sphinxdoc.css
index b680a957103..d0cc2585d20 100644
--- a/package/doc/html/_static/sphinxdoc.css
+++ b/package/doc/html/_static/sphinxdoc.css
@@ -5,7 +5,7 @@
  * Sphinx stylesheet -- sphinxdoc theme.  Originally created by
  * Armin Ronacher for Werkzeug.
  *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -204,20 +204,20 @@ a.headerlink:hover {
     color: white!important;
 }
 
-cite, code, tt {
+cite, code, code {
     font-family: 'Consolas', 'Deja Vu Sans Mono',
                  'Bitstream Vera Sans Mono', monospace;
     font-size: 0.95em;
     letter-spacing: 0.01em;
 }
 
-tt {
+code {
     background-color: #f2f2f2;
     border-bottom: 1px solid #ddd;
     color: #333;
 }
 
-tt.descname, tt.descclassname, tt.xref {
+code.descname, code.descclassname, code.xref {
     border: 0;
 }
 
@@ -226,12 +226,12 @@ hr {
     margin: 2em;
 }
 
-a tt {
+a code {
     border: 0;
     color: #CA7900;
 }
 
-a tt:hover {
+a code:hover {
     color: #2491CF;
 }
 
@@ -336,4 +336,10 @@ div.viewcode-block:target {
     background-color: #f4debf;
     border-top: 1px solid #ac9;
     border-bottom: 1px solid #ac9;
+}
+
+div.code-block-caption {
+    background-color: #ddd;
+    color: #222;
+    border: 1px solid #ccc;
 }
\ No newline at end of file
diff --git a/package/doc/html/_static/underscore-1.3.1.js b/package/doc/html/_static/underscore-1.3.1.js
new file mode 100644
index 00000000000..208d4cd890c
--- /dev/null
+++ b/package/doc/html/_static/underscore-1.3.1.js
@@ -0,0 +1,999 @@
+//     Underscore.js 1.3.1
+//     (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
+//     Underscore is freely distributable under the MIT license.
+//     Portions of Underscore are inspired or borrowed from Prototype,
+//     Oliver Steele's Functional, and John Resig's Micro-Templating.
+//     For all details and documentation:
+//     http://documentcloud.github.com/underscore
+
+(function() {
+
+  // Baseline setup
+  // --------------
+
+  // Establish the root object, `window` in the browser, or `global` on the server.
+  var root = this;
+
+  // Save the previous value of the `_` variable.
+  var previousUnderscore = root._;
+
+  // Establish the object that gets returned to break out of a loop iteration.
+  var breaker = {};
+
+  // Save bytes in the minified (but not gzipped) version:
+  var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
+
+  // Create quick reference variables for speed access to core prototypes.
+  var slice            = ArrayProto.slice,
+      unshift          = ArrayProto.unshift,
+      toString         = ObjProto.toString,
+      hasOwnProperty   = ObjProto.hasOwnProperty;
+
+  // All **ECMAScript 5** native function implementations that we hope to use
+  // are declared here.
+  var
+    nativeForEach      = ArrayProto.forEach,
+    nativeMap          = ArrayProto.map,
+    nativeReduce       = ArrayProto.reduce,
+    nativeReduceRight  = ArrayProto.reduceRight,
+    nativeFilter       = ArrayProto.filter,
+    nativeEvery        = ArrayProto.every,
+    nativeSome         = ArrayProto.some,
+    nativeIndexOf      = ArrayProto.indexOf,
+    nativeLastIndexOf  = ArrayProto.lastIndexOf,
+    nativeIsArray      = Array.isArray,
+    nativeKeys         = Object.keys,
+    nativeBind         = FuncProto.bind;
+
+  // Create a safe reference to the Underscore object for use below.
+  var _ = function(obj) { return new wrapper(obj); };
+
+  // Export the Underscore object for **Node.js**, with
+  // backwards-compatibility for the old `require()` API. If we're in
+  // the browser, add `_` as a global object via a string identifier,
+  // for Closure Compiler "advanced" mode.
+  if (typeof exports !== 'undefined') {
+    if (typeof module !== 'undefined' && module.exports) {
+      exports = module.exports = _;
+    }
+    exports._ = _;
+  } else {
+    root['_'] = _;
+  }
+
+  // Current version.
+  _.VERSION = '1.3.1';
+
+  // Collection Functions
+  // --------------------
+
+  // The cornerstone, an `each` implementation, aka `forEach`.
+  // Handles objects with the built-in `forEach`, arrays, and raw objects.
+  // Delegates to **ECMAScript 5**'s native `forEach` if available.
+  var each = _.each = _.forEach = function(obj, iterator, context) {
+    if (obj == null) return;
+    if (nativeForEach && obj.forEach === nativeForEach) {
+      obj.forEach(iterator, context);
+    } else if (obj.length === +obj.length) {
+      for (var i = 0, l = obj.length; i < l; i++) {
+        if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return;
+      }
+    } else {
+      for (var key in obj) {
+        if (_.has(obj, key)) {
+          if (iterator.call(context, obj[key], key, obj) === breaker) return;
+        }
+      }
+    }
+  };
+
+  // Return the results of applying the iterator to each element.
+  // Delegates to **ECMAScript 5**'s native `map` if available.
+  _.map = _.collect = function(obj, iterator, context) {
+    var results = [];
+    if (obj == null) return results;
+    if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context);
+    each(obj, function(value, index, list) {
+      results[results.length] = iterator.call(context, value, index, list);
+    });
+    if (obj.length === +obj.length) results.length = obj.length;
+    return results;
+  };
+
+  // **Reduce** builds up a single result from a list of values, aka `inject`,
+  // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available.
+  _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) {
+    var initial = arguments.length > 2;
+    if (obj == null) obj = [];
+    if (nativeReduce && obj.reduce === nativeReduce) {
+      if (context) iterator = _.bind(iterator, context);
+      return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator);
+    }
+    each(obj, function(value, index, list) {
+      if (!initial) {
+        memo = value;
+        initial = true;
+      } else {
+        memo = iterator.call(context, memo, value, index, list);
+      }
+    });
+    if (!initial) throw new TypeError('Reduce of empty array with no initial value');
+    return memo;
+  };
+
+  // The right-associative version of reduce, also known as `foldr`.
+  // Delegates to **ECMAScript 5**'s native `reduceRight` if available.
+  _.reduceRight = _.foldr = function(obj, iterator, memo, context) {
+    var initial = arguments.length > 2;
+    if (obj == null) obj = [];
+    if (nativeReduceRight && obj.reduceRight === nativeReduceRight) {
+      if (context) iterator = _.bind(iterator, context);
+      return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator);
+    }
+    var reversed = _.toArray(obj).reverse();
+    if (context && !initial) iterator = _.bind(iterator, context);
+    return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator);
+  };
+
+  // Return the first value which passes a truth test. Aliased as `detect`.
+  _.find = _.detect = function(obj, iterator, context) {
+    var result;
+    any(obj, function(value, index, list) {
+      if (iterator.call(context, value, index, list)) {
+        result = value;
+        return true;
+      }
+    });
+    return result;
+  };
+
+  // Return all the elements that pass a truth test.
+  // Delegates to **ECMAScript 5**'s native `filter` if available.
+  // Aliased as `select`.
+  _.filter = _.select = function(obj, iterator, context) {
+    var results = [];
+    if (obj == null) return results;
+    if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context);
+    each(obj, function(value, index, list) {
+      if (iterator.call(context, value, index, list)) results[results.length] = value;
+    });
+    return results;
+  };
+
+  // Return all the elements for which a truth test fails.
+  _.reject = function(obj, iterator, context) {
+    var results = [];
+    if (obj == null) return results;
+    each(obj, function(value, index, list) {
+      if (!iterator.call(context, value, index, list)) results[results.length] = value;
+    });
+    return results;
+  };
+
+  // Determine whether all of the elements match a truth test.
+  // Delegates to **ECMAScript 5**'s native `every` if available.
+  // Aliased as `all`.
+  _.every = _.all = function(obj, iterator, context) {
+    var result = true;
+    if (obj == null) return result;
+    if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context);
+    each(obj, function(value, index, list) {
+      if (!(result = result && iterator.call(context, value, index, list))) return breaker;
+    });
+    return result;
+  };
+
+  // Determine if at least one element in the object matches a truth test.
+  // Delegates to **ECMAScript 5**'s native `some` if available.
+  // Aliased as `any`.
+  var any = _.some = _.any = function(obj, iterator, context) {
+    iterator || (iterator = _.identity);
+    var result = false;
+    if (obj == null) return result;
+    if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context);
+    each(obj, function(value, index, list) {
+      if (result || (result = iterator.call(context, value, index, list))) return breaker;
+    });
+    return !!result;
+  };
+
+  // Determine if a given value is included in the array or object using `===`.
+  // Aliased as `contains`.
+  _.include = _.contains = function(obj, target) {
+    var found = false;
+    if (obj == null) return found;
+    if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1;
+    found = any(obj, function(value) {
+      return value === target;
+    });
+    return found;
+  };
+
+  // Invoke a method (with arguments) on every item in a collection.
+  _.invoke = function(obj, method) {
+    var args = slice.call(arguments, 2);
+    return _.map(obj, function(value) {
+      return (_.isFunction(method) ? method || value : value[method]).apply(value, args);
+    });
+  };
+
+  // Convenience version of a common use case of `map`: fetching a property.
+  _.pluck = function(obj, key) {
+    return _.map(obj, function(value){ return value[key]; });
+  };
+
+  // Return the maximum element or (element-based computation).
+  _.max = function(obj, iterator, context) {
+    if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj);
+    if (!iterator && _.isEmpty(obj)) return -Infinity;
+    var result = {computed : -Infinity};
+    each(obj, function(value, index, list) {
+      var computed = iterator ? iterator.call(context, value, index, list) : value;
+      computed >= result.computed && (result = {value : value, computed : computed});
+    });
+    return result.value;
+  };
+
+  // Return the minimum element (or element-based computation).
+  _.min = function(obj, iterator, context) {
+    if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj);
+    if (!iterator && _.isEmpty(obj)) return Infinity;
+    var result = {computed : Infinity};
+    each(obj, function(value, index, list) {
+      var computed = iterator ? iterator.call(context, value, index, list) : value;
+      computed < result.computed && (result = {value : value, computed : computed});
+    });
+    return result.value;
+  };
+
+  // Shuffle an array.
+  _.shuffle = function(obj) {
+    var shuffled = [], rand;
+    each(obj, function(value, index, list) {
+      if (index == 0) {
+        shuffled[0] = value;
+      } else {
+        rand = Math.floor(Math.random() * (index + 1));
+        shuffled[index] = shuffled[rand];
+        shuffled[rand] = value;
+      }
+    });
+    return shuffled;
+  };
+
+  // Sort the object's values by a criterion produced by an iterator.
+  _.sortBy = function(obj, iterator, context) {
+    return _.pluck(_.map(obj, function(value, index, list) {
+      return {
+        value : value,
+        criteria : iterator.call(context, value, index, list)
+      };
+    }).sort(function(left, right) {
+      var a = left.criteria, b = right.criteria;
+      return a < b ? -1 : a > b ? 1 : 0;
+    }), 'value');
+  };
+
+  // Groups the object's values by a criterion. Pass either a string attribute
+  // to group by, or a function that returns the criterion.
+  _.groupBy = function(obj, val) {
+    var result = {};
+    var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; };
+    each(obj, function(value, index) {
+      var key = iterator(value, index);
+      (result[key] || (result[key] = [])).push(value);
+    });
+    return result;
+  };
+
+  // Use a comparator function to figure out at what index an object should
+  // be inserted so as to maintain order. Uses binary search.
+  _.sortedIndex = function(array, obj, iterator) {
+    iterator || (iterator = _.identity);
+    var low = 0, high = array.length;
+    while (low < high) {
+      var mid = (low + high) >> 1;
+      iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid;
+    }
+    return low;
+  };
+
+  // Safely convert anything iterable into a real, live array.
+  _.toArray = function(iterable) {
+    if (!iterable)                return [];
+    if (iterable.toArray)         return iterable.toArray();
+    if (_.isArray(iterable))      return slice.call(iterable);
+    if (_.isArguments(iterable))  return slice.call(iterable);
+    return _.values(iterable);
+  };
+
+  // Return the number of elements in an object.
+  _.size = function(obj) {
+    return _.toArray(obj).length;
+  };
+
+  // Array Functions
+  // ---------------
+
+  // Get the first element of an array. Passing **n** will return the first N
+  // values in the array. Aliased as `head`. The **guard** check allows it to work
+  // with `_.map`.
+  _.first = _.head = function(array, n, guard) {
+    return (n != null) && !guard ? slice.call(array, 0, n) : array[0];
+  };
+
+  // Returns everything but the last entry of the array. Especcialy useful on
+  // the arguments object. Passing **n** will return all the values in
+  // the array, excluding the last N. The **guard** check allows it to work with
+  // `_.map`.
+  _.initial = function(array, n, guard) {
+    return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n));
+  };
+
+  // Get the last element of an array. Passing **n** will return the last N
+  // values in the array. The **guard** check allows it to work with `_.map`.
+  _.last = function(array, n, guard) {
+    if ((n != null) && !guard) {
+      return slice.call(array, Math.max(array.length - n, 0));
+    } else {
+      return array[array.length - 1];
+    }
+  };
+
+  // Returns everything but the first entry of the array. Aliased as `tail`.
+  // Especially useful on the arguments object. Passing an **index** will return
+  // the rest of the values in the array from that index onward. The **guard**
+  // check allows it to work with `_.map`.
+  _.rest = _.tail = function(array, index, guard) {
+    return slice.call(array, (index == null) || guard ? 1 : index);
+  };
+
+  // Trim out all falsy values from an array.
+  _.compact = function(array) {
+    return _.filter(array, function(value){ return !!value; });
+  };
+
+  // Return a completely flattened version of an array.
+  _.flatten = function(array, shallow) {
+    return _.reduce(array, function(memo, value) {
+      if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value));
+      memo[memo.length] = value;
+      return memo;
+    }, []);
+  };
+
+  // Return a version of the array that does not contain the specified value(s).
+  _.without = function(array) {
+    return _.difference(array, slice.call(arguments, 1));
+  };
+
+  // Produce a duplicate-free version of the array. If the array has already
+  // been sorted, you have the option of using a faster algorithm.
+  // Aliased as `unique`.
+  _.uniq = _.unique = function(array, isSorted, iterator) {
+    var initial = iterator ? _.map(array, iterator) : array;
+    var result = [];
+    _.reduce(initial, function(memo, el, i) {
+      if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) {
+        memo[memo.length] = el;
+        result[result.length] = array[i];
+      }
+      return memo;
+    }, []);
+    return result;
+  };
+
+  // Produce an array that contains the union: each distinct element from all of
+  // the passed-in arrays.
+  _.union = function() {
+    return _.uniq(_.flatten(arguments, true));
+  };
+
+  // Produce an array that contains every item shared between all the
+  // passed-in arrays. (Aliased as "intersect" for back-compat.)
+  _.intersection = _.intersect = function(array) {
+    var rest = slice.call(arguments, 1);
+    return _.filter(_.uniq(array), function(item) {
+      return _.every(rest, function(other) {
+        return _.indexOf(other, item) >= 0;
+      });
+    });
+  };
+
+  // Take the difference between one array and a number of other arrays.
+  // Only the elements present in just the first array will remain.
+  _.difference = function(array) {
+    var rest = _.flatten(slice.call(arguments, 1));
+    return _.filter(array, function(value){ return !_.include(rest, value); });
+  };
+
+  // Zip together multiple lists into a single array -- elements that share
+  // an index go together.
+  _.zip = function() {
+    var args = slice.call(arguments);
+    var length = _.max(_.pluck(args, 'length'));
+    var results = new Array(length);
+    for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i);
+    return results;
+  };
+
+  // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**),
+  // we need this function. Return the position of the first occurrence of an
+  // item in an array, or -1 if the item is not included in the array.
+  // Delegates to **ECMAScript 5**'s native `indexOf` if available.
+  // If the array is large and already in sort order, pass `true`
+  // for **isSorted** to use binary search.
+  _.indexOf = function(array, item, isSorted) {
+    if (array == null) return -1;
+    var i, l;
+    if (isSorted) {
+      i = _.sortedIndex(array, item);
+      return array[i] === item ? i : -1;
+    }
+    if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item);
+    for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i;
+    return -1;
+  };
+
+  // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available.
+  _.lastIndexOf = function(array, item) {
+    if (array == null) return -1;
+    if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item);
+    var i = array.length;
+    while (i--) if (i in array && array[i] === item) return i;
+    return -1;
+  };
+
+  // Generate an integer Array containing an arithmetic progression. A port of
+  // the native Python `range()` function. See
+  // [the Python documentation](http://docs.python.org/library/functions.html#range).
+  _.range = function(start, stop, step) {
+    if (arguments.length <= 1) {
+      stop = start || 0;
+      start = 0;
+    }
+    step = arguments[2] || 1;
+
+    var len = Math.max(Math.ceil((stop - start) / step), 0);
+    var idx = 0;
+    var range = new Array(len);
+
+    while(idx < len) {
+      range[idx++] = start;
+      start += step;
+    }
+
+    return range;
+  };
+
+  // Function (ahem) Functions
+  // ------------------
+
+  // Reusable constructor function for prototype setting.
+  var ctor = function(){};
+
+  // Create a function bound to a given object (assigning `this`, and arguments,
+  // optionally). Binding with arguments is also known as `curry`.
+  // Delegates to **ECMAScript 5**'s native `Function.bind` if available.
+  // We check for `func.bind` first, to fail fast when `func` is undefined.
+  _.bind = function bind(func, context) {
+    var bound, args;
+    if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
+    if (!_.isFunction(func)) throw new TypeError;
+    args = slice.call(arguments, 2);
+    return bound = function() {
+      if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));
+      ctor.prototype = func.prototype;
+      var self = new ctor;
+      var result = func.apply(self, args.concat(slice.call(arguments)));
+      if (Object(result) === result) return result;
+      return self;
+    };
+  };
+
+  // Bind all of an object's methods to that object. Useful for ensuring that
+  // all callbacks defined on an object belong to it.
+  _.bindAll = function(obj) {
+    var funcs = slice.call(arguments, 1);
+    if (funcs.length == 0) funcs = _.functions(obj);
+    each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); });
+    return obj;
+  };
+
+  // Memoize an expensive function by storing its results.
+  _.memoize = function(func, hasher) {
+    var memo = {};
+    hasher || (hasher = _.identity);
+    return function() {
+      var key = hasher.apply(this, arguments);
+      return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments));
+    };
+  };
+
+  // Delays a function for the given number of milliseconds, and then calls
+  // it with the arguments supplied.
+  _.delay = function(func, wait) {
+    var args = slice.call(arguments, 2);
+    return setTimeout(function(){ return func.apply(func, args); }, wait);
+  };
+
+  // Defers a function, scheduling it to run after the current call stack has
+  // cleared.
+  _.defer = function(func) {
+    return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
+  };
+
+  // Returns a function, that, when invoked, will only be triggered at most once
+  // during a given window of time.
+  _.throttle = function(func, wait) {
+    var context, args, timeout, throttling, more;
+    var whenDone = _.debounce(function(){ more = throttling = false; }, wait);
+    return function() {
+      context = this; args = arguments;
+      var later = function() {
+        timeout = null;
+        if (more) func.apply(context, args);
+        whenDone();
+      };
+      if (!timeout) timeout = setTimeout(later, wait);
+      if (throttling) {
+        more = true;
+      } else {
+        func.apply(context, args);
+      }
+      whenDone();
+      throttling = true;
+    };
+  };
+
+  // Returns a function, that, as long as it continues to be invoked, will not
+  // be triggered. The function will be called after it stops being called for
+  // N milliseconds.
+  _.debounce = function(func, wait) {
+    var timeout;
+    return function() {
+      var context = this, args = arguments;
+      var later = function() {
+        timeout = null;
+        func.apply(context, args);
+      };
+      clearTimeout(timeout);
+      timeout = setTimeout(later, wait);
+    };
+  };
+
+  // Returns a function that will be executed at most one time, no matter how
+  // often you call it. Useful for lazy initialization.
+  _.once = function(func) {
+    var ran = false, memo;
+    return function() {
+      if (ran) return memo;
+      ran = true;
+      return memo = func.apply(this, arguments);
+    };
+  };
+
+  // Returns the first function passed as an argument to the second,
+  // allowing you to adjust arguments, run code before and after, and
+  // conditionally execute the original function.
+  _.wrap = function(func, wrapper) {
+    return function() {
+      var args = [func].concat(slice.call(arguments, 0));
+      return wrapper.apply(this, args);
+    };
+  };
+
+  // Returns a function that is the composition of a list of functions, each
+  // consuming the return value of the function that follows.
+  _.compose = function() {
+    var funcs = arguments;
+    return function() {
+      var args = arguments;
+      for (var i = funcs.length - 1; i >= 0; i--) {
+        args = [funcs[i].apply(this, args)];
+      }
+      return args[0];
+    };
+  };
+
+  // Returns a function that will only be executed after being called N times.
+  _.after = function(times, func) {
+    if (times <= 0) return func();
+    return function() {
+      if (--times < 1) { return func.apply(this, arguments); }
+    };
+  };
+
+  // Object Functions
+  // ----------------
+
+  // Retrieve the names of an object's properties.
+  // Delegates to **ECMAScript 5**'s native `Object.keys`
+  _.keys = nativeKeys || function(obj) {
+    if (obj !== Object(obj)) throw new TypeError('Invalid object');
+    var keys = [];
+    for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key;
+    return keys;
+  };
+
+  // Retrieve the values of an object's properties.
+  _.values = function(obj) {
+    return _.map(obj, _.identity);
+  };
+
+  // Return a sorted list of the function names available on the object.
+  // Aliased as `methods`
+  _.functions = _.methods = function(obj) {
+    var names = [];
+    for (var key in obj) {
+      if (_.isFunction(obj[key])) names.push(key);
+    }
+    return names.sort();
+  };
+
+  // Extend a given object with all the properties in passed-in object(s).
+  _.extend = function(obj) {
+    each(slice.call(arguments, 1), function(source) {
+      for (var prop in source) {
+        obj[prop] = source[prop];
+      }
+    });
+    return obj;
+  };
+
+  // Fill in a given object with default properties.
+  _.defaults = function(obj) {
+    each(slice.call(arguments, 1), function(source) {
+      for (var prop in source) {
+        if (obj[prop] == null) obj[prop] = source[prop];
+      }
+    });
+    return obj;
+  };
+
+  // Create a (shallow-cloned) duplicate of an object.
+  _.clone = function(obj) {
+    if (!_.isObject(obj)) return obj;
+    return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
+  };
+
+  // Invokes interceptor with the obj, and then returns obj.
+  // The primary purpose of this method is to "tap into" a method chain, in
+  // order to perform operations on intermediate results within the chain.
+  _.tap = function(obj, interceptor) {
+    interceptor(obj);
+    return obj;
+  };
+
+  // Internal recursive comparison function.
+  function eq(a, b, stack) {
+    // Identical objects are equal. `0 === -0`, but they aren't identical.
+    // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
+    if (a === b) return a !== 0 || 1 / a == 1 / b;
+    // A strict comparison is necessary because `null == undefined`.
+    if (a == null || b == null) return a === b;
+    // Unwrap any wrapped objects.
+    if (a._chain) a = a._wrapped;
+    if (b._chain) b = b._wrapped;
+    // Invoke a custom `isEqual` method if one is provided.
+    if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b);
+    if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a);
+    // Compare `[[Class]]` names.
+    var className = toString.call(a);
+    if (className != toString.call(b)) return false;
+    switch (className) {
+      // Strings, numbers, dates, and booleans are compared by value.
+      case '[object String]':
+        // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
+        // equivalent to `new String("5")`.
+        return a == String(b);
+      case '[object Number]':
+        // `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for
+        // other numeric values.
+        return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b);
+      case '[object Date]':
+      case '[object Boolean]':
+        // Coerce dates and booleans to numeric primitive values. Dates are compared by their
+        // millisecond representations. Note that invalid dates with millisecond representations
+        // of `NaN` are not equivalent.
+        return +a == +b;
+      // RegExps are compared by their source patterns and flags.
+      case '[object RegExp]':
+        return a.source == b.source &&
+               a.global == b.global &&
+               a.multiline == b.multiline &&
+               a.ignoreCase == b.ignoreCase;
+    }
+    if (typeof a != 'object' || typeof b != 'object') return false;
+    // Assume equality for cyclic structures. The algorithm for detecting cyclic
+    // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
+    var length = stack.length;
+    while (length--) {
+      // Linear search. Performance is inversely proportional to the number of
+      // unique nested structures.
+      if (stack[length] == a) return true;
+    }
+    // Add the first object to the stack of traversed objects.
+    stack.push(a);
+    var size = 0, result = true;
+    // Recursively compare objects and arrays.
+    if (className == '[object Array]') {
+      // Compare array lengths to determine if a deep comparison is necessary.
+      size = a.length;
+      result = size == b.length;
+      if (result) {
+        // Deep compare the contents, ignoring non-numeric properties.
+        while (size--) {
+          // Ensure commutative equality for sparse arrays.
+          if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break;
+        }
+      }
+    } else {
+      // Objects with different constructors are not equivalent.
+      if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false;
+      // Deep compare objects.
+      for (var key in a) {
+        if (_.has(a, key)) {
+          // Count the expected number of properties.
+          size++;
+          // Deep compare each member.
+          if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break;
+        }
+      }
+      // Ensure that both objects contain the same number of properties.
+      if (result) {
+        for (key in b) {
+          if (_.has(b, key) && !(size--)) break;
+        }
+        result = !size;
+      }
+    }
+    // Remove the first object from the stack of traversed objects.
+    stack.pop();
+    return result;
+  }
+
+  // Perform a deep comparison to check if two objects are equal.
+  _.isEqual = function(a, b) {
+    return eq(a, b, []);
+  };
+
+  // Is a given array, string, or object empty?
+  // An "empty" object has no enumerable own-properties.
+  _.isEmpty = function(obj) {
+    if (_.isArray(obj) || _.isString(obj)) return obj.length === 0;
+    for (var key in obj) if (_.has(obj, key)) return false;
+    return true;
+  };
+
+  // Is a given value a DOM element?
+  _.isElement = function(obj) {
+    return !!(obj && obj.nodeType == 1);
+  };
+
+  // Is a given value an array?
+  // Delegates to ECMA5's native Array.isArray
+  _.isArray = nativeIsArray || function(obj) {
+    return toString.call(obj) == '[object Array]';
+  };
+
+  // Is a given variable an object?
+  _.isObject = function(obj) {
+    return obj === Object(obj);
+  };
+
+  // Is a given variable an arguments object?
+  _.isArguments = function(obj) {
+    return toString.call(obj) == '[object Arguments]';
+  };
+  if (!_.isArguments(arguments)) {
+    _.isArguments = function(obj) {
+      return !!(obj && _.has(obj, 'callee'));
+    };
+  }
+
+  // Is a given value a function?
+  _.isFunction = function(obj) {
+    return toString.call(obj) == '[object Function]';
+  };
+
+  // Is a given value a string?
+  _.isString = function(obj) {
+    return toString.call(obj) == '[object String]';
+  };
+
+  // Is a given value a number?
+  _.isNumber = function(obj) {
+    return toString.call(obj) == '[object Number]';
+  };
+
+  // Is the given value `NaN`?
+  _.isNaN = function(obj) {
+    // `NaN` is the only value for which `===` is not reflexive.
+    return obj !== obj;
+  };
+
+  // Is a given value a boolean?
+  _.isBoolean = function(obj) {
+    return obj === true || obj === false || toString.call(obj) == '[object Boolean]';
+  };
+
+  // Is a given value a date?
+  _.isDate = function(obj) {
+    return toString.call(obj) == '[object Date]';
+  };
+
+  // Is the given value a regular expression?
+  _.isRegExp = function(obj) {
+    return toString.call(obj) == '[object RegExp]';
+  };
+
+  // Is a given value equal to null?
+  _.isNull = function(obj) {
+    return obj === null;
+  };
+
+  // Is a given variable undefined?
+  _.isUndefined = function(obj) {
+    return obj === void 0;
+  };
+
+  // Has own property?
+  _.has = function(obj, key) {
+    return hasOwnProperty.call(obj, key);
+  };
+
+  // Utility Functions
+  // -----------------
+
+  // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
+  // previous owner. Returns a reference to the Underscore object.
+  _.noConflict = function() {
+    root._ = previousUnderscore;
+    return this;
+  };
+
+  // Keep the identity function around for default iterators.
+  _.identity = function(value) {
+    return value;
+  };
+
+  // Run a function **n** times.
+  _.times = function (n, iterator, context) {
+    for (var i = 0; i < n; i++) iterator.call(context, i);
+  };
+
+  // Escape a string for HTML interpolation.
+  _.escape = function(string) {
+    return (''+string).replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;').replace(/"/g, '&quot;').replace(/'/g, '&#x27;').replace(/\//g,'&#x2F;');
+  };
+
+  // Add your own custom functions to the Underscore object, ensuring that
+  // they're correctly added to the OOP wrapper as well.
+  _.mixin = function(obj) {
+    each(_.functions(obj), function(name){
+      addToWrapper(name, _[name] = obj[name]);
+    });
+  };
+
+  // Generate a unique integer id (unique within the entire client session).
+  // Useful for temporary DOM ids.
+  var idCounter = 0;
+  _.uniqueId = function(prefix) {
+    var id = idCounter++;
+    return prefix ? prefix + id : id;
+  };
+
+  // By default, Underscore uses ERB-style template delimiters, change the
+  // following template settings to use alternative delimiters.
+  _.templateSettings = {
+    evaluate    : /<%([\s\S]+?)%>/g,
+    interpolate : /<%=([\s\S]+?)%>/g,
+    escape      : /<%-([\s\S]+?)%>/g
+  };
+
+  // When customizing `templateSettings`, if you don't want to define an
+  // interpolation, evaluation or escaping regex, we need one that is
+  // guaranteed not to match.
+  var noMatch = /.^/;
+
+  // Within an interpolation, evaluation, or escaping, remove HTML escaping
+  // that had been previously added.
+  var unescape = function(code) {
+    return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'");
+  };
+
+  // JavaScript micro-templating, similar to John Resig's implementation.
+  // Underscore templating handles arbitrary delimiters, preserves whitespace,
+  // and correctly escapes quotes within interpolated code.
+  _.template = function(str, data) {
+    var c  = _.templateSettings;
+    var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' +
+      'with(obj||{}){__p.push(\'' +
+      str.replace(/\\/g, '\\\\')
+         .replace(/'/g, "\\'")
+         .replace(c.escape || noMatch, function(match, code) {
+           return "',_.escape(" + unescape(code) + "),'";
+         })
+         .replace(c.interpolate || noMatch, function(match, code) {
+           return "'," + unescape(code) + ",'";
+         })
+         .replace(c.evaluate || noMatch, function(match, code) {
+           return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('";
+         })
+         .replace(/\r/g, '\\r')
+         .replace(/\n/g, '\\n')
+         .replace(/\t/g, '\\t')
+         + "');}return __p.join('');";
+    var func = new Function('obj', '_', tmpl);
+    if (data) return func(data, _);
+    return function(data) {
+      return func.call(this, data, _);
+    };
+  };
+
+  // Add a "chain" function, which will delegate to the wrapper.
+  _.chain = function(obj) {
+    return _(obj).chain();
+  };
+
+  // The OOP Wrapper
+  // ---------------
+
+  // If Underscore is called as a function, it returns a wrapped object that
+  // can be used OO-style. This wrapper holds altered versions of all the
+  // underscore functions. Wrapped objects may be chained.
+  var wrapper = function(obj) { this._wrapped = obj; };
+
+  // Expose `wrapper.prototype` as `_.prototype`
+  _.prototype = wrapper.prototype;
+
+  // Helper function to continue chaining intermediate results.
+  var result = function(obj, chain) {
+    return chain ? _(obj).chain() : obj;
+  };
+
+  // A method to easily add functions to the OOP wrapper.
+  var addToWrapper = function(name, func) {
+    wrapper.prototype[name] = function() {
+      var args = slice.call(arguments);
+      unshift.call(args, this._wrapped);
+      return result(func.apply(_, args), this._chain);
+    };
+  };
+
+  // Add all of the Underscore functions to the wrapper object.
+  _.mixin(_);
+
+  // Add all mutator Array functions to the wrapper.
+  each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
+    var method = ArrayProto[name];
+    wrapper.prototype[name] = function() {
+      var wrapped = this._wrapped;
+      method.apply(wrapped, arguments);
+      var length = wrapped.length;
+      if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0];
+      return result(wrapped, this._chain);
+    };
+  });
+
+  // Add all accessor Array functions to the wrapper.
+  each(['concat', 'join', 'slice'], function(name) {
+    var method = ArrayProto[name];
+    wrapper.prototype[name] = function() {
+      return result(method.apply(this._wrapped, arguments), this._chain);
+    };
+  });
+
+  // Start chaining a wrapped Underscore object.
+  wrapper.prototype.chain = function() {
+    this._chain = true;
+    return this;
+  };
+
+  // Extracts the result from a wrapped and chained object.
+  wrapper.prototype.value = function() {
+    return this._wrapped;
+  };
+
+}).call(this);
diff --git a/package/doc/html/_static/underscore.js b/package/doc/html/_static/underscore.js
index 5d89914340f..5b55f32beac 100644
--- a/package/doc/html/_static/underscore.js
+++ b/package/doc/html/_static/underscore.js
@@ -1,23 +1,31 @@
-// Underscore.js 0.5.5
-// (c) 2009 Jeremy Ashkenas, DocumentCloud Inc.
-// Underscore is freely distributable under the terms of the MIT license.
-// Portions of Underscore are inspired by or borrowed from Prototype.js,
+// Underscore.js 1.3.1
+// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the MIT license.
+// Portions of Underscore are inspired or borrowed from Prototype,
 // Oliver Steele's Functional, and John Resig's Micro-Templating.
 // For all details and documentation:
-// http://documentcloud.github.com/underscore/
-(function(){var j=this,n=j._,i=function(a){this._wrapped=a},m=typeof StopIteration!=="undefined"?StopIteration:"__break__",b=j._=function(a){return new i(a)};if(typeof exports!=="undefined")exports._=b;var k=Array.prototype.slice,o=Array.prototype.unshift,p=Object.prototype.toString,q=Object.prototype.hasOwnProperty,r=Object.prototype.propertyIsEnumerable;b.VERSION="0.5.5";b.each=function(a,c,d){try{if(a.forEach)a.forEach(c,d);else if(b.isArray(a)||b.isArguments(a))for(var e=0,f=a.length;e<f;e++)c.call(d,
-a[e],e,a);else{var g=b.keys(a);f=g.length;for(e=0;e<f;e++)c.call(d,a[g[e]],g[e],a)}}catch(h){if(h!=m)throw h;}return a};b.map=function(a,c,d){if(a&&b.isFunction(a.map))return a.map(c,d);var e=[];b.each(a,function(f,g,h){e.push(c.call(d,f,g,h))});return e};b.reduce=function(a,c,d,e){if(a&&b.isFunction(a.reduce))return a.reduce(b.bind(d,e),c);b.each(a,function(f,g,h){c=d.call(e,c,f,g,h)});return c};b.reduceRight=function(a,c,d,e){if(a&&b.isFunction(a.reduceRight))return a.reduceRight(b.bind(d,e),c);
-var f=b.clone(b.toArray(a)).reverse();b.each(f,function(g,h){c=d.call(e,c,g,h,a)});return c};b.detect=function(a,c,d){var e;b.each(a,function(f,g,h){if(c.call(d,f,g,h)){e=f;b.breakLoop()}});return e};b.select=function(a,c,d){if(a&&b.isFunction(a.filter))return a.filter(c,d);var e=[];b.each(a,function(f,g,h){c.call(d,f,g,h)&&e.push(f)});return e};b.reject=function(a,c,d){var e=[];b.each(a,function(f,g,h){!c.call(d,f,g,h)&&e.push(f)});return e};b.all=function(a,c,d){c=c||b.identity;if(a&&b.isFunction(a.every))return a.every(c,
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diff --git a/package/doc/html/_static/up-pressed.png b/package/doc/html/_static/up-pressed.png
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index e9bd1b851c6..28d65db4aaf 100644
--- a/package/doc/html/_static/websupport.js
+++ b/package/doc/html/_static/websupport.js
@@ -4,7 +4,7 @@
  *
  * sphinx.websupport utilties for all documentation.
  *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -50,51 +50,51 @@
   }
 
   function initEvents() {
-    $('a.comment-close').live("click", function(event) {
+    $(document).on("click", 'a.comment-close', function(event) {
       event.preventDefault();
       hide($(this).attr('id').substring(2));
     });
-    $('a.vote').live("click", function(event) {
+    $(document).on("click", 'a.vote', function(event) {
       event.preventDefault();
       handleVote($(this));
     });
-    $('a.reply').live("click", function(event) {
+    $(document).on("click", 'a.reply', function(event) {
       event.preventDefault();
       openReply($(this).attr('id').substring(2));
     });
-    $('a.close-reply').live("click", function(event) {
+    $(document).on("click", 'a.close-reply', function(event) {
       event.preventDefault();
       closeReply($(this).attr('id').substring(2));
     });
-    $('a.sort-option').live("click", function(event) {
+    $(document).on("click", 'a.sort-option', function(event) {
       event.preventDefault();
       handleReSort($(this));
     });
-    $('a.show-proposal').live("click", function(event) {
+    $(document).on("click", 'a.show-proposal', function(event) {
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     });
-    $('a.hide-proposal').live("click", function(event) {
+    $(document).on("click", 'a.hide-proposal', function(event) {
       event.preventDefault();
       hideProposal($(this).attr('id').substring(2));
     });
-    $('a.show-propose-change').live("click", function(event) {
+    $(document).on("click", 'a.show-propose-change', function(event) {
       event.preventDefault();
       showProposeChange($(this).attr('id').substring(2));
     });
-    $('a.hide-propose-change').live("click", function(event) {
+    $(document).on("click", 'a.hide-propose-change', function(event) {
       event.preventDefault();
       hideProposeChange($(this).attr('id').substring(2));
     });
-    $('a.accept-comment').live("click", function(event) {
+    $(document).on("click", 'a.accept-comment', function(event) {
       event.preventDefault();
       acceptComment($(this).attr('id').substring(2));
     });
-    $('a.delete-comment').live("click", function(event) {
+    $(document).on("click", 'a.delete-comment', function(event) {
       event.preventDefault();
       deleteComment($(this).attr('id').substring(2));
     });
-    $('a.comment-markup').live("click", function(event) {
+    $(document).on("click", 'a.comment-markup', function(event) {
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@@ -700,8 +700,8 @@
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       <div class="comment-markup-box" id="mb<%id%>">\
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-        <tt>``code``</tt>, \
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+        <code>``code``</code>, \
+        code blocks: <code>::</code> and an indented block after blank line</div>\
       <form method="post" id="cf<%id%>" class="comment-form" action="">\
         <textarea name="comment" cols="80"></textarea>\
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diff --git a/package/doc/html/documentation_pages/analysis/align.html b/package/doc/html/documentation_pages/analysis/align.html
index d6da633eba0..a179dbb28e4 100644
--- a/package/doc/html/documentation_pages/analysis/align.html
+++ b/package/doc/html/documentation_pages/analysis/align.html
@@ -1,5 +1,3 @@
-
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@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.1.1. Coordinate fitting and alignment — MDAnalysis.analysis.align &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.1.1. Coordinate fitting and alignment — MDAnalysis.analysis.align &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
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@@ -16,7 +14,7 @@
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       var DOCUMENTATION_OPTIONS = {
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-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
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     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="3.1.2. Native contacts analysis — MDAnalysis.analysis.contacts" href="contacts.html" />
     <link rel="prev" title="3. Analysis modules" href="../analysis_modules.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../analysis_modules.html" title="3. Analysis modules"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.1.1. Coordinate fitting and alignment &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.align</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.1.1. Coordinate fitting and alignment &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.align</span></code></a><ul>
 <li><a class="reference internal" href="#rms-fitting-tutorial">3.1.1.1. RMS-fitting tutorial</a></li>
 <li><a class="reference internal" href="#common-usage">3.1.1.2. Common usage</a></li>
 <li><a class="reference internal" href="#functions">3.1.1.3. Functions</a></li>
@@ -76,13 +74,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">3. Analysis modules</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="contacts.html"
-                        title="next chapter">3.1.2. Native contacts analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/analysis/align.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">3.1.2. Native contacts analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/analysis/align.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -101,10 +101,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.align"></span><div class="section" id="coordinate-fitting-and-alignment-mdanalysis-analysis-align">
-<h1>3.1.1. Coordinate fitting and alignment &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.align" title="MDAnalysis.analysis.align"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.align</span></tt></a><a class="headerlink" href="#coordinate-fitting-and-alignment-mdanalysis-analysis-align" title="Permalink to this headline">¶</a></h1>
+<h1>3.1.1. Coordinate fitting and alignment &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.align" title="MDAnalysis.analysis.align"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.align</span></code></a><a class="headerlink" href="#coordinate-fitting-and-alignment-mdanalysis-analysis-align" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -119,33 +119,33 @@ <h1>3.1.1. Coordinate fitting and alignment &#8212; <a class="reference internal
 </table>
 <p>The module contains functions to fit a target structure to a reference
 structure. They use the fast QCP algorithm to calculate the root mean
-square distance (RMSD) between two coordinate sets <a class="reference internal" href="../lib/qcprot.html#theobald2005">[Theobald2005]</a> and
-the rotation matrix <em>R</em> that minimizes the RMSD <a class="reference internal" href="../lib/qcprot.html#liu2010">[Liu2010]</a>. (Please
+square distance (RMSD) between two coordinate sets <a class="reference internal" href="../lib/qcprot.html#theobald2005" id="id1">[Theobald2005]</a> and
+the rotation matrix <em>R</em> that minimizes the RMSD <a class="reference internal" href="../lib/qcprot.html#liu2010" id="id2">[Liu2010]</a>. (Please
 cite these references when using this module.).</p>
 <p>Typically, one selects a group of atoms (such as the C-alphas),
 calculates the RMSD and transformation matrix, and applys the
 transformation to the current frame of a trajectory to obtain the
-rotated structure. The <a class="reference internal" href="#MDAnalysis.analysis.align.alignto" title="MDAnalysis.analysis.align.alignto"><tt class="xref py py-func docutils literal"><span class="pre">alignto()</span></tt></a> and <a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><tt class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></tt></a>
+rotated structure. The <a class="reference internal" href="#MDAnalysis.analysis.align.alignto" title="MDAnalysis.analysis.align.alignto"><code class="xref py py-func docutils literal"><span class="pre">alignto()</span></code></a> and <a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><code class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></code></a>
 functions can be used to do this for individual frames and
 trajectories respectively.</p>
-<p>The <a class="reference internal" href="#rms-fitting-tutorial"><em>RMS-fitting tutorial</em></a> shows how to do the individual steps
+<p>The <a class="reference internal" href="#rms-fitting-tutorial"><span>RMS-fitting tutorial</span></a> shows how to do the individual steps
 manually and explains the intermediate steps.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <dl class="last docutils">
-<dt><a class="reference internal" href="rms.html#module-MDAnalysis.analysis.rms" title="MDAnalysis.analysis.rms"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></tt></a></dt>
+<dt><a class="reference internal" href="rms.html#module-MDAnalysis.analysis.rms" title="MDAnalysis.analysis.rms"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></code></a></dt>
 <dd>contains functions to compute RMSD (when structural alignment is not
 required)</dd>
-<dt><a class="reference internal" href="../lib/qcprot.html#module-MDAnalysis.lib.qcprot" title="MDAnalysis.lib.qcprot"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></tt></a></dt>
+<dt><a class="reference internal" href="../lib/qcprot.html#module-MDAnalysis.lib.qcprot" title="MDAnalysis.lib.qcprot"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></code></a></dt>
 <dd>implements the fast RMSD algorithm.</dd>
 </dl>
 </div>
 <div class="section" id="rms-fitting-tutorial">
 <span id="id3"></span><h2>3.1.1.1. RMS-fitting tutorial<a class="headerlink" href="#rms-fitting-tutorial" title="Permalink to this headline">¶</a></h2>
 <p>The example uses files provided as part of the MDAnalysis test suite
-(in the variables <tt class="xref py py-data docutils literal"><span class="pre">PSF</span></tt>,
-<tt class="xref py py-data docutils literal"><span class="pre">DCD</span></tt>, and
-<tt class="xref py py-data docutils literal"><span class="pre">PDB_small</span></tt>). For all further
+(in the variables <code class="xref py py-data docutils literal"><span class="pre">PSF</span></code>,
+<code class="xref py py-data docutils literal"><span class="pre">DCD</span></code>, and
+<code class="xref py py-data docutils literal"><span class="pre">PDB_small</span></code>). For all further
 examples execute first</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">MDAnalysis</span> <span class="kn">import</span> <span class="o">*</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">MDAnalysis.analysis.align</span> <span class="kn">import</span> <span class="o">*</span>
@@ -154,24 +154,24 @@ <h1>3.1.1. Coordinate fitting and alignment &#8212; <a class="reference internal
 </pre></div>
 </div>
 <p>In the simplest case, we can simply calculate the C-alpha RMSD between
-two structures, using <tt class="xref py py-func docutils literal"><span class="pre">rmsd()</span></tt>:</p>
+two structures, using <code class="xref py py-func docutils literal"><span class="pre">rmsd()</span></code>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">ref</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PDB_small</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">mobile</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">rmsd</span><span class="p">(</span><span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">coordinates</span><span class="p">(),</span> <span class="n">ref</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">coordinates</span><span class="p">())</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">rmsd</span><span class="p">(</span><span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">positions</span><span class="p">,</span> <span class="n">ref</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">positions</span><span class="p">)</span>
 <span class="go">18.858259026820352</span>
 </pre></div>
 </div>
 <p>Note that in this example translations have not been removed. In order
 to look at the pure rotation one needs to superimpose the centres of
 mass (or geometry) first:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">ref0</span> <span class="o">=</span>  <span class="n">ref</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span> <span class="o">-</span> <span class="n">ref</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">mobile0</span> <span class="o">=</span> <span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span> <span class="o">-</span> <span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">ref0</span> <span class="o">=</span>  <span class="n">ref</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">positions</span> <span class="o">-</span> <span class="n">ref</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">mobile0</span> <span class="o">=</span> <span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">positions</span> <span class="o">-</span> <span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">rmsd</span><span class="p">(</span><span class="n">mobile0</span><span class="p">,</span> <span class="n">ref0</span><span class="p">)</span>
 <span class="go"> 6.8093965864717951</span>
 </pre></div>
 </div>
 <p>The rotation matrix that superimposes <em>mobile</em> on <em>ref</em> while
-minimizing the CA-RMSD is obtained with the <a class="reference internal" href="#MDAnalysis.analysis.align.rotation_matrix" title="MDAnalysis.analysis.align.rotation_matrix"><tt class="xref py py-func docutils literal"><span class="pre">rotation_matrix()</span></tt></a>
+minimizing the CA-RMSD is obtained with the <a class="reference internal" href="#MDAnalysis.analysis.align.rotation_matrix" title="MDAnalysis.analysis.align.rotation_matrix"><code class="xref py py-func docutils literal"><span class="pre">rotation_matrix()</span></code></a>
 function</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">R</span><span class="p">,</span> <span class="n">rmsd</span> <span class="o">=</span> <span class="n">rotation_matrix</span><span class="p">(</span><span class="n">mobile0</span><span class="p">,</span> <span class="n">ref0</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="k">print</span> <span class="n">rmsd</span>
@@ -183,16 +183,16 @@ <h1>3.1.1. Coordinate fitting and alignment &#8212; <a class="reference internal
 </pre></div>
 </div>
 <p>Putting all this together one can superimpose all of <em>mobile</em> onto <em>ref</em>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span><span class="o">-</span><span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">())</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span><span class="o">-</span><span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">())</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">rotate</span><span class="p">(</span><span class="n">R</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span><span class="n">ref</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">())</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span><span class="n">ref</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">CA</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">())</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">mobile</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&quot;mobile_on_ref.pdb&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
 <div class="section" id="common-usage">
 <h2>3.1.1.2. Common usage<a class="headerlink" href="#common-usage" title="Permalink to this headline">¶</a></h2>
-<p>To <strong>fit a single structure</strong> with <a class="reference internal" href="#MDAnalysis.analysis.align.alignto" title="MDAnalysis.analysis.align.alignto"><tt class="xref py py-func docutils literal"><span class="pre">alignto()</span></tt></a>:</p>
+<p>To <strong>fit a single structure</strong> with <a class="reference internal" href="#MDAnalysis.analysis.align.alignto" title="MDAnalysis.analysis.align.alignto"><code class="xref py py-func docutils literal"><span class="pre">alignto()</span></code></a>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">ref</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span> <span class="n">PDB_small</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">mobile</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span> <span class="n">DCD</span><span class="p">)</span>     <span class="c"># we use the first frame</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">alignto</span><span class="p">(</span><span class="n">mobile</span><span class="p">,</span> <span class="n">ref</span><span class="p">,</span> <span class="n">select</span><span class="o">=</span><span class="s">&quot;protein and name CA&quot;</span><span class="p">,</span> <span class="n">mass_weighted</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
@@ -201,7 +201,7 @@ <h2>3.1.1.2. Common usage<a class="headerlink" href="#common-usage" title="Perma
 <p>This will change <em>all</em> coordinates in <em>mobile</em> so that the protein
 C-alpha atoms are optimally superimposed (translation and rotation).</p>
 <p>To <strong>fit a whole trajectory</strong> to a reference structure with the
-<a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><tt class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></tt></a> function:</p>
+<a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><code class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></code></a> function:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">ref</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span> <span class="n">PDB_small</span><span class="p">)</span>   <span class="c"># reference structure 1AKE</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">trj</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span> <span class="n">DCD</span><span class="p">)</span>         <span class="c"># trajectory of change 1AKE-&gt;4AKE</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">rms_fit_trj</span><span class="p">(</span><span class="n">trj</span><span class="p">,</span> <span class="n">ref</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="s">&#39;rmsfit.dcd&#39;</span><span class="p">)</span>
@@ -211,8 +211,8 @@ <h2>3.1.1.2. Common usage<a class="headerlink" href="#common-usage" title="Perma
 mapping between atoms based on a sequence alignment. This allows
 fitting of structural homologs or wild type and mutant.</p>
 <p>If a alignment was provided as &#8220;sequences.aln&#8221; one would first produce
-the appropriate MDAnalysis selections with the <a class="reference internal" href="#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><tt class="xref py py-func docutils literal"><span class="pre">fasta2select()</span></tt></a>
-function and then feed the resulting dictionary to <a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><tt class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></tt></a>:</p>
+the appropriate MDAnalysis selections with the <a class="reference internal" href="#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><code class="xref py py-func docutils literal"><span class="pre">fasta2select()</span></code></a>
+function and then feed the resulting dictionary to <a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><code class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></code></a>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">seldict</span> <span class="o">=</span> <span class="n">fasta2select</span><span class="p">(</span><span class="s">&#39;sequences.aln&#39;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">rms_fit_trj</span><span class="p">(</span><span class="n">trj</span><span class="p">,</span> <span class="n">ref</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="s">&#39;rmsfit.dcd&#39;</span><span class="p">,</span> <span class="n">select</span><span class="o">=</span><span class="n">seldict</span><span class="p">)</span>
 </pre></div>
@@ -223,7 +223,7 @@ <h2>3.1.1.2. Common usage<a class="headerlink" href="#common-usage" title="Perma
 <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.analysis.align.alignto">
-<tt class="descclassname">MDAnalysis.analysis.align.</tt><tt class="descname">alignto</tt><big>(</big><em>mobile</em>, <em>reference</em>, <em>select='all'</em>, <em>mass_weighted=False</em>, <em>subselection=None</em>, <em>tol_mass=0.1</em>, <em>strict=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/align.html#alignto"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.align.alignto" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.align.</code><code class="descname">alignto</code><span class="sig-paren">(</span><em>mobile</em>, <em>reference</em>, <em>select='all'</em>, <em>mass_weighted=False</em>, <em>subselection=None</em>, <em>tol_mass=0.1</em>, <em>strict=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/align.html#alignto"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.align.alignto" title="Permalink to this definition">¶</a></dt>
 <dd><p>Spatially align <em>mobile</em> to <em>reference</em> by doing a RMSD fit on <em>select</em> atoms.</p>
 <p>The superposition is done in the following way:</p>
 <ol class="arabic simple">
@@ -233,19 +233,19 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 translated so that its center of geometry (or center of mass)
 coincides with the one of <em>reference</em>. (See below for explanation of
 how <em>sel1</em> and <em>sel2</em> are derived from <em>select</em>.)</li>
-<li>All atoms in <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> that
+<li>All atoms in <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> that
 contains <em>mobile</em> are shifted and rotated. (See below for how
 to change this behavior through the <em>subselection</em> keyword.)</li>
 </ol>
 <p>The <em>mobile</em> and <em>reference</em> atom groups can be constructed so that they
 already match atom by atom. In this case, <em>select</em> should be set to &#8220;all&#8221;
-(or <tt class="docutils literal"><span class="pre">None</span></tt>) so that no further selections are applied to <em>mobile</em> and
+(or <code class="docutils literal"><span class="pre">None</span></code>) so that no further selections are applied to <em>mobile</em> and
 <em>reference</em>, therefore preserving the exact atom ordering (see
-<a class="reference internal" href="../selections.html#ordered-selections-label"><em>Ordered selections</em></a>).</p>
+<a class="reference internal" href="../selections.html#ordered-selections-label"><span>Ordered selections</span></a>).</p>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
 <p class="last">The atom order for <em>mobile</em> and <em>reference</em> is <em>only</em>
-preserved when <em>select</em> is either &#8220;all&#8221; or <tt class="docutils literal"><span class="pre">None</span></tt>. In any other case,
+preserved when <em>select</em> is either &#8220;all&#8221; or <code class="docutils literal"><span class="pre">None</span></code>. In any other case,
 a new selection will be made that will sort the resulting AtomGroup by
 index and therefore destroy the correspondence between the two groups. <strong>It
 is safest not to mix ordered AtomGroups with selection strings.</strong></p>
@@ -254,31 +254,31 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>mobile</em></dt>
-<dd><p class="first last">structure to be aligned, a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
-or a whole <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a></p>
+<dd><p class="first last">structure to be aligned, a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+or a whole <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a></p>
 </dd>
 <dt><em>reference</em></dt>
-<dd><p class="first last">reference structure, a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
-or a whole <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a></p>
+<dd><p class="first last">reference structure, a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+or a whole <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a></p>
 </dd>
 <dt><em>select</em></dt>
 <dd><ol class="first arabic simple">
 <li>any valid selection string for
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> that produces identical
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> that produces identical
 selections in <em>mobile</em> and <em>reference</em>; or</li>
-<li>dictionary <tt class="docutils literal"><span class="pre">{'mobile':sel1,</span> <span class="pre">'reference':sel2}</span></tt>.
-(the <a class="reference internal" href="#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><tt class="xref py py-func docutils literal"><span class="pre">fasta2select()</span></tt></a> function returns such a
+<li>dictionary <code class="docutils literal"><span class="pre">{'mobile':sel1,</span> <span class="pre">'reference':sel2}</span></code>.
+(the <a class="reference internal" href="#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><code class="xref py py-func docutils literal"><span class="pre">fasta2select()</span></code></a> function returns such a
 dictionary based on a <a class="reference external" href="http://www.clustal.org/">ClustalW</a> or <a class="reference external" href="http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/">STAMP</a> sequence alignment); or</li>
-<li>tuple <tt class="docutils literal"><span class="pre">(sel1,</span> <span class="pre">sel2)</span></tt></li>
+<li>tuple <code class="docutils literal"><span class="pre">(sel1,</span> <span class="pre">sel2)</span></code></li>
 </ol>
 <p class="last">When using 2. or 3. with <em>sel1</em> and <em>sel2</em> then these selections can also each be
 a list of selection strings (to generate a AtomGroup with defined atom order as
-described under <a class="reference internal" href="../selections.html#ordered-selections-label"><em>Ordered selections</em></a>).</p>
+described under <a class="reference internal" href="../selections.html#ordered-selections-label"><span>Ordered selections</span></a>).</p>
 </dd>
 <dt><em>mass_weighted</em> <span class="classifier-delimiter">:</span> <span class="classifier">boolean</span></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt> uses the masses <tt class="xref py py-meth docutils literal"><span class="pre">reference.masses()</span></tt> as weights for the
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code> uses the masses <code class="xref py py-meth docutils literal"><span class="pre">reference.masses()</span></code> as weights for the
 RMSD fit.</p>
 </dd>
 <dt><em>tol_mass</em></dt>
@@ -287,13 +287,13 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 </dd>
 <dt><em>strict</em></dt>
 <dd><dl class="first last docutils">
-<dt><tt class="docutils literal"><span class="pre">True</span></tt></dt>
-<dd><p class="first last">Will raise <tt class="xref py py-exc docutils literal"><span class="pre">SelectioError</span></tt> if a single atom does not
+<dt><code class="docutils literal"><span class="pre">True</span></code></dt>
+<dd><p class="first last">Will raise <code class="xref py py-exc docutils literal"><span class="pre">SelectioError</span></code> if a single atom does not
 match between the two selections.</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">False</span></tt> [default]</dt>
+<dt><code class="docutils literal"><span class="pre">False</span></code> [default]</dt>
 <dd><p class="first last">Will try to prepare a matching selection by dropping
-residues with non-matching atoms. See <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><tt class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></tt></a>
+residues with non-matching atoms. See <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><code class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></code></a>
 for details.</p>
 </dd>
 </dl>
@@ -301,7 +301,7 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 <dt><em>subselection</em></dt>
 <dd><p class="first">Apply the transformation only to this selection.</p>
 <dl class="last docutils">
-<dt><tt class="docutils literal"><span class="pre">None</span></tt> [default]</dt>
+<dt><code class="docutils literal"><span class="pre">None</span></code> [default]</dt>
 <dd><p class="first last">Apply to <cite>mobile.universe.atoms</cite> (i.e. all atoms in the
 context of the selection from <em>mobile</em> such as the rest of a
 protein, ligands and the surrounding water)</p>
@@ -309,7 +309,7 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 <dt><em>selection-string</em></dt>
 <dd><p class="first last">Apply to <cite>mobile.select_atoms(selection-string)</cite></p>
 </dd>
-<dt><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></dt>
+<dt><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a></dt>
 <dd><p class="first last">Apply to the arbitrary group of atoms</p>
 </dd>
 </dl>
@@ -317,31 +317,33 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">RMSD before and after spatial alignment.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">RMSD before and after spatial alignment.</p>
 </td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">For RMSD-fitting trajectories it is more efficient to
-use <a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><tt class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></tt></a>.</p>
+use <a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><code class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></code></a>.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added check that the two groups describe the same atoms including
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added check that the two groups describe the same atoms including
 the new <em>tol_mass</em> keyword.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Uses <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><tt class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></tt></a> to work with incomplete selections
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Uses <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><code class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></code></a> to work with incomplete selections
 and new <em>strict</em> keyword. The new default is to be lenient whereas
-the old behavior was the equivalent of <em>strict</em> = <tt class="docutils literal"><span class="pre">True</span></tt>.</p>
+the old behavior was the equivalent of <em>strict</em> = <code class="docutils literal"><span class="pre">True</span></code>.</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.align.rms_fit_trj">
-<tt class="descclassname">MDAnalysis.analysis.align.</tt><tt class="descname">rms_fit_trj</tt><big>(</big><em>traj</em>, <em>reference</em>, <em>select='all'</em>, <em>filename=None</em>, <em>rmsdfile=None</em>, <em>prefix='rmsfit_'</em>, <em>mass_weighted=False</em>, <em>tol_mass=0.1</em>, <em>strict=False</em>, <em>force=True</em>, <em>quiet=False</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/align.html#rms_fit_trj"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.align.rms_fit_trj" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.align.</code><code class="descname">rms_fit_trj</code><span class="sig-paren">(</span><em>traj</em>, <em>reference</em>, <em>select='all'</em>, <em>filename=None</em>, <em>rmsdfile=None</em>, <em>prefix='rmsfit_'</em>, <em>mass_weighted=False</em>, <em>tol_mass=0.1</em>, <em>strict=False</em>, <em>force=True</em>, <em>quiet=False</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/align.html#rms_fit_trj"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.align.rms_fit_trj" title="Permalink to this definition">¶</a></dt>
 <dd><p>RMS-fit trajectory to a reference structure using a selection.</p>
 <p>Both reference <em>ref</em> and trajectory <em>traj</em> must be
-<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> instances. If they contain a
+<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> instances. If they contain a
 trajectory then it is used. The output file format is determined
 by the file extension of <em>filename</em>. One can also use the same
 universe if one wants to fit to the current frame.</p>
@@ -349,34 +351,34 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>traj</em></dt>
-<dd><p class="first last">trajectory, <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object</p>
+<dd><p class="first last">trajectory, <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object</p>
 </dd>
 <dt><em>reference</em></dt>
-<dd><p class="first last">reference coordinates; <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object
+<dd><p class="first last">reference coordinates; <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object
 (uses the current time step of the object)</p>
 </dd>
 <dt><em>select</em></dt>
 <dd><ol class="first arabic simple">
 <li>any valid selection string for
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> that produces identical
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> that produces identical
 selections in <em>mobile</em> and <em>reference</em>; or</li>
-<li>a dictionary <tt class="docutils literal"><span class="pre">{'mobile':sel1,</span> <span class="pre">'reference':sel2}</span></tt> (the
-<a class="reference internal" href="#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><tt class="xref py py-func docutils literal"><span class="pre">fasta2select()</span></tt></a> function returns such a
+<li>a dictionary <code class="docutils literal"><span class="pre">{'mobile':sel1,</span> <span class="pre">'reference':sel2}</span></code> (the
+<a class="reference internal" href="#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><code class="xref py py-func docutils literal"><span class="pre">fasta2select()</span></code></a> function returns such a
 dictionary based on a <a class="reference external" href="http://www.clustal.org/">ClustalW</a> or <a class="reference external" href="http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/">STAMP</a> sequence alignment); or</li>
-<li>a tuple <tt class="docutils literal"><span class="pre">(sel1,</span> <span class="pre">sel2)</span></tt></li>
+<li>a tuple <code class="docutils literal"><span class="pre">(sel1,</span> <span class="pre">sel2)</span></code></li>
 </ol>
 <p class="last">When using 2. or 3. with <em>sel1</em> and <em>sel2</em> then these selections can also each be
 a list of selection strings (to generate a AtomGroup with defined atom order as
-described under <a class="reference internal" href="../selections.html#ordered-selections-label"><em>Ordered selections</em></a>).</p>
+described under <a class="reference internal" href="../selections.html#ordered-selections-label"><span>Ordered selections</span></a>).</p>
 </dd>
 <dt><em>filename</em></dt>
 <dd><p class="first last">file name for the RMS-fitted trajectory or pdb; defaults to the
 original trajectory filename (from <em>traj</em>) with <em>prefix</em> prepended</p>
 </dd>
 <dt><em>rmsdfile</em></dt>
-<dd><p class="first last">file name for writing the RMSD timeseries [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">file name for writing the RMSD timeseries [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>prefix</em></dt>
 <dd><p class="first last">prefix for autogenerating the new output filename</p>
@@ -389,27 +391,27 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 <em>tol_mass</em> [0.1]</p>
 </dd>
 <dt><em>strict</em></dt>
-<dd><p class="first">Default: <tt class="docutils literal"><span class="pre">False</span></tt>
-- <tt class="docutils literal"><span class="pre">True</span></tt>: Will raise <tt class="xref py py-exc docutils literal"><span class="pre">SelectioError</span></tt> if a single atom does not</p>
+<dd><p class="first">Default: <code class="docutils literal"><span class="pre">False</span></code>
+- <code class="docutils literal"><span class="pre">True</span></code>: Will raise <code class="xref py py-exc docutils literal"><span class="pre">SelectioError</span></code> if a single atom does not</p>
 <blockquote>
 <div><p>match between the two selections.</p>
 </div></blockquote>
 <ul class="last simple">
-<li><tt class="docutils literal"><span class="pre">False</span></tt>: Will try to prepare a matching selection by dropping
-residues with non-matching atoms. See <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><tt class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></tt></a>
+<li><code class="docutils literal"><span class="pre">False</span></code>: Will try to prepare a matching selection by dropping
+residues with non-matching atoms. See <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><code class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></code></a>
 for details.</li>
 </ul>
 </dd>
 <dt><em>force</em></dt>
 <dd><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">True</span></tt>: Overwrite an existing output trajectory (default)</li>
-<li><tt class="docutils literal"><span class="pre">False</span></tt>: simply return if the file already exists</li>
+<li><code class="docutils literal"><span class="pre">True</span></code>: Overwrite an existing output trajectory (default)</li>
+<li><code class="docutils literal"><span class="pre">False</span></code>: simply return if the file already exists</li>
 </ul>
 </dd>
 <dt><em>quiet</em></dt>
 <dd><ul class="first simple">
-<li><tt class="docutils literal"><span class="pre">True</span></tt>: suppress progress and logging for levels INFO and below.</li>
-<li><tt class="docutils literal"><span class="pre">False</span></tt>: show all status messages and do not change the the logging
+<li><code class="docutils literal"><span class="pre">True</span></code>: suppress progress and logging for levels INFO and below.</li>
+<li><code class="docutils literal"><span class="pre">False</span></code>: show all status messages and do not change the the logging
 level (default)</li>
 </ul>
 <div class="last admonition note">
@@ -419,30 +421,32 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 </dd>
 <dt><em>kwargs</em></dt>
 <dd><p class="first last">All other keyword arguments are passed on the trajectory
-<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Writer" title="MDAnalysis.coordinates.base.Writer"><tt class="xref py py-class docutils literal"><span class="pre">Writer</span></tt></a>; this allows manipulating/fixing
+<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Writer" title="MDAnalysis.coordinates.base.Writer"><code class="xref py py-class docutils literal"><span class="pre">Writer</span></code></a>; this allows manipulating/fixing
 trajectories on the fly (e.g. change the output format by changing the extension of <em>filename</em>
 and setting different parameters as described for the corresponding writer).</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><em>filename</em> (either provided or auto-generated)</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><em>filename</em> (either provided or auto-generated)</p>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added <em>kwargs</em> to be passed to the trajectory <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Writer" title="MDAnalysis.coordinates.base.Writer"><tt class="xref py py-class docutils literal"><span class="pre">Writer</span></tt></a> and
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>kwargs</em> to be passed to the trajectory <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Writer" title="MDAnalysis.coordinates.base.Writer"><code class="xref py py-class docutils literal"><span class="pre">Writer</span></code></a> and
 <em>filename</em> is returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Uses <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><tt class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></tt></a> to work with incomplete selections
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Uses <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><code class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></code></a> to work with incomplete selections
 and new <em>strict</em> keyword. The new default is to be lenient whereas
-the old behavior was the equivalent of <em>strict</em> = <tt class="docutils literal"><span class="pre">True</span></tt>.</p>
+the old behavior was the equivalent of <em>strict</em> = <code class="docutils literal"><span class="pre">True</span></code>.</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.align.rotation_matrix">
-<tt class="descclassname">MDAnalysis.analysis.align.</tt><tt class="descname">rotation_matrix</tt><big>(</big><em>a</em>, <em>b</em>, <em>weights=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/align.html#rotation_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.align.rotation_matrix" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.align.</code><code class="descname">rotation_matrix</code><span class="sig-paren">(</span><em>a</em>, <em>b</em>, <em>weights=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/align.html#rotation_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.align.rotation_matrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns the 3x3 rotation matrix for RMSD fitting coordinate sets <em>a</em> and <em>b</em>.</p>
 <p>The rotation matrix <em>R</em> transforms <em>a</em> to overlap with <em>b</em> (i.e. <em>b</em> is the
 reference structure):</p>
@@ -452,15 +456,15 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>a</em></dt>
 <dd><p class="first last">coordinates that are to be rotated (&#8220;mobile set&#8221;); array of N atoms
 of shape N*3 as generated by, e.g.,
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.coordinates()</span></tt></a>.</p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.coordinates()</span></code></a>.</p>
 </dd>
 <dt><em>b</em></dt>
 <dd><p class="first last">reference coordinates; array of N atoms of shape N*3 as generated by,
-e.g., <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.coordinates()</span></tt></a>.</p>
+e.g., <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.coordinates()</span></code></a>.</p>
 </dd>
 <dt><em>weights</em></dt>
 <dd><p class="first last">array of floats of size N for doing weighted RMSD fitting (e.g. the
@@ -469,13 +473,13 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><tt class="docutils literal"><span class="pre">(R,</span> <span class="pre">rmsd)</span></tt> rmsd and rotation matrix <em>R</em></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="docutils literal"><span class="pre">(R,</span> <span class="pre">rmsd)</span></code> rmsd and rotation matrix <em>R</em></p>
 </td>
 </tr>
 </tbody>
 </table>
 <p><em>R</em> can be used as an argument for
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.rotate" title="MDAnalysis.core.AtomGroup.AtomGroup.rotate"><tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.rotate()</span></tt></a> to generate a rotated
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.rotate" title="MDAnalysis.core.AtomGroup.AtomGroup.rotate"><code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.rotate()</span></code></a> to generate a rotated
 selection, e.g.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">R</span> <span class="o">=</span> <span class="n">rotation_matrix</span><span class="p">(</span><span class="n">A</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&#39;backbone&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">coordinates</span><span class="p">(),</span> <span class="n">B</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&#39;backbone&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">coordinates</span><span class="p">())</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">A</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">rotate</span><span class="p">(</span><span class="n">R</span><span class="p">)</span>
@@ -484,19 +488,20 @@ <h2>3.1.1.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 </div>
 <p>Note that the function does <em>not</em> shift the centers of mass or geometry;
 this needs to be done by the user.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-func docutils literal"><span class="pre">rmsd()</span></tt> calculates the RMSD between <em>a</em> and <em>b</em>; for
+<p class="last"><code class="xref py py-func docutils literal"><span class="pre">rmsd()</span></code> calculates the RMSD between <em>a</em> and <em>b</em>; for
 fitting a whole trajectory it is more efficient to use
-<a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><tt class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></tt></a>. A complete fit of two structures can be
-done with <a class="reference internal" href="#MDAnalysis.analysis.align.alignto" title="MDAnalysis.analysis.align.alignto"><tt class="xref py py-func docutils literal"><span class="pre">alignto()</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><code class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></code></a>. A complete fit of two structures can be
+done with <a class="reference internal" href="#MDAnalysis.analysis.align.alignto" title="MDAnalysis.analysis.align.alignto"><code class="xref py py-func docutils literal"><span class="pre">alignto()</span></code></a>.</p>
 </div>
 </dd></dl>
 
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Function <a class="reference internal" href="rms.html#MDAnalysis.analysis.rms.rmsd" title="MDAnalysis.analysis.rms.rmsd"><tt class="xref py py-func docutils literal"><span class="pre">rmsd()</span></tt></a> was removed from
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Function <a class="reference internal" href="rms.html#MDAnalysis.analysis.rms.rmsd" title="MDAnalysis.analysis.rms.rmsd"><code class="xref py py-func docutils literal"><span class="pre">rmsd()</span></code></a> was removed from
 this module and is now exclusively accessible as
-<a class="reference internal" href="rms.html#MDAnalysis.analysis.rms.rmsd" title="MDAnalysis.analysis.rms.rmsd"><tt class="xref py py-func docutils literal"><span class="pre">rmsd()</span></tt></a>.</p>
+<a class="reference internal" href="rms.html#MDAnalysis.analysis.rms.rmsd" title="MDAnalysis.analysis.rms.rmsd"><code class="xref py py-func docutils literal"><span class="pre">rmsd()</span></code></a>.</p>
+</div>
 </div>
 <div class="section" id="helper-functions">
 <h2>3.1.1.4. Helper functions<a class="headerlink" href="#helper-functions" title="Permalink to this headline">¶</a></h2>
@@ -505,7 +510,7 @@ <h2>3.1.1.4. Helper functions<a class="headerlink" href="#helper-functions" titl
 normal users.</p>
 <dl class="function">
 <dt id="MDAnalysis.analysis.align.fasta2select">
-<tt class="descclassname">MDAnalysis.analysis.align.</tt><tt class="descname">fasta2select</tt><big>(</big><em>fastafilename</em>, <em>is_aligned=False</em>, <em>ref_resids=None</em>, <em>target_resids=None</em>, <em>ref_offset=0</em>, <em>target_offset=0</em>, <em>verbosity=3</em>, <em>alnfilename=None</em>, <em>treefilename=None</em>, <em>clustalw='clustalw2'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/align.html#fasta2select"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.align.fasta2select" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.align.</code><code class="descname">fasta2select</code><span class="sig-paren">(</span><em>fastafilename</em>, <em>is_aligned=False</em>, <em>ref_resids=None</em>, <em>target_resids=None</em>, <em>ref_offset=0</em>, <em>target_offset=0</em>, <em>verbosity=3</em>, <em>alnfilename=None</em>, <em>treefilename=None</em>, <em>clustalw='clustalw2'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/align.html#fasta2select"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.align.fasta2select" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return selection strings that will select equivalent residues.</p>
 <p>The function aligns two sequences provided in a FASTA file and
 constructs MDAnalysis selection strings of the common atoms. When
@@ -532,14 +537,14 @@ <h2>3.1.1.4. Helper functions<a class="headerlink" href="#helper-functions" titl
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>fastafilename</em></dt>
 <dd><p class="first last">FASTA file with first sequence as reference and
 second the one to be aligned (ORDER IS IMPORTANT!)</p>
 </dd>
 <dt><em>is_aligned</em></dt>
 <dd><p class="first last">False: run clustalw for sequence alignment; True: use
-the alignment in the file (e.g. from STAMP) [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+the alignment in the file (e.g. from STAMP) [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>ref_offset</em></dt>
 <dd><p class="first last">add this number to the column number in the FASTA file
@@ -556,27 +561,27 @@ <h2>3.1.1.4. Helper functions<a class="headerlink" href="#helper-functions" titl
 </dd>
 <dt><em>alnfilename</em></dt>
 <dd><p class="first last">filename of ClustalW alignment (clustal format) that is
-produced by <em>clustalw</em> when <em>is_aligned</em> = <tt class="docutils literal"><span class="pre">False</span></tt>.
-<tt class="docutils literal"><span class="pre">None</span></tt> uses the name and path of <em>fastafilename</em> and
-subsititutes the suffix with &#8216;.aln&#8217;.[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+produced by <em>clustalw</em> when <em>is_aligned</em> = <code class="docutils literal"><span class="pre">False</span></code>.
+<code class="docutils literal"><span class="pre">None</span></code> uses the name and path of <em>fastafilename</em> and
+subsititutes the suffix with &#8216;.aln&#8217;.[<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>treefilename</em></dt>
 <dd><p class="first last">filename of ClustalW guide tree (Newick format);
-if <tt class="docutils literal"><span class="pre">None</span></tt>  the the filename is generated from <em>alnfilename</em>
-with the suffix &#8216;.dnd&#8217; instead of &#8216;.aln&#8217; [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+if <code class="docutils literal"><span class="pre">None</span></code>  the the filename is generated from <em>alnfilename</em>
+with the suffix &#8216;.dnd&#8217; instead of &#8216;.aln&#8217; [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>clustalw</em></dt>
 <dd><p class="first last">path to the ClustalW (or ClustalW2) binary; only
-needed for <em>is_aligned</em> = <tt class="docutils literal"><span class="pre">False</span></tt> [&#8220;clustalw2&#8221;]</p>
+needed for <em>is_aligned</em> = <code class="docutils literal"><span class="pre">False</span></code> [&#8220;clustalw2&#8221;]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>select_dict</em></dt>
 <dd><p class="first last">dictionary with &#8216;reference&#8217; and &#8216;mobile&#8217; selection string
-that can be used immediately in <a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><tt class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></tt></a> as
-<tt class="docutils literal"><span class="pre">select=select_dict</span></tt>.</p>
+that can be used immediately in <a class="reference internal" href="#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><code class="xref py py-func docutils literal"><span class="pre">rms_fit_trj()</span></code></a> as
+<code class="docutils literal"><span class="pre">select=select_dict</span></code>.</p>
 </dd>
 </dl>
 </td>
@@ -587,47 +592,47 @@ <h2>3.1.1.4. Helper functions<a class="headerlink" href="#helper-functions" titl
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.align.get_matching_atoms">
-<tt class="descclassname">MDAnalysis.analysis.align.</tt><tt class="descname">get_matching_atoms</tt><big>(</big><em>ag1</em>, <em>ag2</em>, <em>tol_mass=0.1</em>, <em>strict=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/align.html#get_matching_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.align.get_matching_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.align.</code><code class="descname">get_matching_atoms</code><span class="sig-paren">(</span><em>ag1</em>, <em>ag2</em>, <em>tol_mass=0.1</em>, <em>strict=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/align.html#get_matching_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.align.get_matching_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return two atom groups with one-to-one matched atoms.</p>
-<p>The function takes two <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
+<p>The function takes two <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
 instances <em>ag1</em> and <em>ag2</em> and returns two atom groups <em>g1</em> and <em>g2</em> that
-consist of atoms so that the mass of atom <tt class="docutils literal"><span class="pre">g1[0]</span></tt> is the same as the mass
-of atom <tt class="docutils literal"><span class="pre">g2[0]</span></tt>, <tt class="docutils literal"><span class="pre">g1[1]</span></tt> and <tt class="docutils literal"><span class="pre">g2[1]</span></tt> etc.</p>
+consist of atoms so that the mass of atom <code class="docutils literal"><span class="pre">g1[0]</span></code> is the same as the mass
+of atom <code class="docutils literal"><span class="pre">g2[0]</span></code>, <code class="docutils literal"><span class="pre">g1[1]</span></code> and <code class="docutils literal"><span class="pre">g2[1]</span></code> etc.</p>
 <p>The current implementation is very simplistic and works on a per-residue basis:</p>
 <ol class="arabic simple">
 <li>The two groups must contain the same number of residues.</li>
 <li>Any residues in each group that have differing number of atoms are discarded.</li>
 <li>The masses of corresponding atoms are compared. and if any masses differ
 by more than <em>tol_mass</em> the test is considered failed and a
-<tt class="xref py py-exc docutils literal"><span class="pre">SelectionError</span></tt> is raised.</li>
+<code class="xref py py-exc docutils literal"><span class="pre">SelectionError</span></code> is raised.</li>
 </ol>
-<p>The log file (see <a class="reference internal" href="../lib/log.html#MDAnalysis.start_logging" title="MDAnalysis.start_logging"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.start_logging()</span></tt></a>) will contain detailed
+<p>The log file (see <a class="reference internal" href="../lib/log.html#MDAnalysis.start_logging" title="MDAnalysis.start_logging"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.start_logging()</span></code></a>) will contain detailed
 information about mismatches.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>ag1</em>, <em>ag2</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> instances that are compared</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> instances that are compared</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>tol_mass</em></dt>
 <dd><p class="first last">Reject if the atomic masses for matched atoms differ by more than
 <em>tol_mass</em> [0.1]</p>
 </dd>
 <dt><em>strict</em></dt>
 <dd><dl class="first last docutils">
-<dt><tt class="docutils literal"><span class="pre">True</span></tt></dt>
-<dd><p class="first last">Will raise <tt class="xref py py-exc docutils literal"><span class="pre">SelectioError</span></tt> if a single atom does not
+<dt><code class="docutils literal"><span class="pre">True</span></code></dt>
+<dd><p class="first last">Will raise <code class="xref py py-exc docutils literal"><span class="pre">SelectioError</span></code> if a single atom does not
 match between the two selections.</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">False</span></tt> [default]</dt>
+<dt><code class="docutils literal"><span class="pre">False</span></code> [default]</dt>
 <dd><p class="first last">Will try to prepare a matching selection by dropping
-residues with non-matching atoms. See <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><tt class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></tt></a>
+residues with non-matching atoms. See <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><code class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></code></a>
 for details.</p>
 </dd>
 </dl>
@@ -635,25 +640,27 @@ <h2>3.1.1.4. Helper functions<a class="headerlink" href="#helper-functions" titl
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">Tuple <tt class="docutils literal"><span class="pre">(g1,</span> <span class="pre">g2)</span></tt> with <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> instances
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Tuple <code class="docutils literal"><span class="pre">(g1,</span> <span class="pre">g2)</span></code> with <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> instances
 that match, atom by atom. The groups are either the original groups if all matches
 or slices of the original groups.</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">SelectionError</span></tt> if the number of residues does not match or if in the final
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">SelectionError</span></code> if the number of residues does not match or if in the final
 matching masses differ by more than <em>tol</em>.</p>
 </td>
 </tr>
 </tbody>
 </table>
 <p>The algorithm could be improved by using e.g. the Needleman-Wunsch
-algorithm in <tt class="xref py py-mod docutils literal"><span class="pre">Bio.profile2</span></tt> to align atoms in each residue (doing a
+algorithm in <code class="xref py py-mod docutils literal"><span class="pre">Bio.profile2</span></code> to align atoms in each residue (doing a
 global alignment is too expensive).</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Renamed from <tt class="xref py py-func docutils literal"><span class="pre">check_same_atoms()</span></tt> to <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><tt class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></tt></a> and now returns
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Renamed from <code class="xref py py-func docutils literal"><span class="pre">check_same_atoms()</span></code> to <a class="reference internal" href="#MDAnalysis.analysis.align.get_matching_atoms" title="MDAnalysis.analysis.align.get_matching_atoms"><code class="xref py py-func docutils literal"><span class="pre">get_matching_atoms()</span></code></a> and now returns
 matching atomgroups (possibly with residues removed)</p>
+</div>
 </dd></dl>
 
 </div>
@@ -665,7 +672,7 @@ <h2>3.1.1.4. Helper functions<a class="headerlink" href="#helper-functions" titl
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -680,11 +687,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../analysis_modules.html" title="3. Analysis modules"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -694,7 +701,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/contacts.html b/package/doc/html/documentation_pages/analysis/contacts.html
index c65096682ac..4a2c861a99f 100644
--- a/package/doc/html/documentation_pages/analysis/contacts.html
+++ b/package/doc/html/documentation_pages/analysis/contacts.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.1.2. Native contacts analysis — MDAnalysis.analysis.contacts &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.1.2. Native contacts analysis — MDAnalysis.analysis.contacts &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="3.1.3. Distance analysis — MDAnalysis.analysis.distances" href="distances.html" />
     <link rel="prev" title="3.1.1. Coordinate fitting and alignment — MDAnalysis.analysis.align" href="align.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="align.html" title="3.1.1. Coordinate fitting and alignment — MDAnalysis.analysis.align"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.1.2. Native contacts analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.1.2. Native contacts analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></code></a><ul>
 <li><a class="reference internal" href="#examples">3.1.2.1. Examples</a><ul>
 <li><a class="reference internal" href="#one-dimensional-contact-analysis">3.1.2.1.1. One-dimensional contact analysis</a></li>
 <li><a class="reference internal" href="#two-dimensional-contact-analysis-q1-q2">3.1.2.1.2. Two-dimensional contact analysis (q1-q2)</a></li>
@@ -75,16 +73,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="align.html"
-                        title="previous chapter">3.1.1. Coordinate fitting and alignment &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.analysis.align</span></tt></a></p>
+                        title="previous chapter">3.1.1. Coordinate fitting and alignment &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.align</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="distances.html"
-                        title="next chapter">3.1.3. Distance analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.distances</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/analysis/contacts.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">3.1.3. Distance analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.distances</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/analysis/contacts.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -103,10 +103,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.contacts"></span><div class="section" id="native-contacts-analysis-mdanalysis-analysis-contacts">
-<h1>3.1.2. Native contacts analysis &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.contacts" title="MDAnalysis.analysis.contacts"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></tt></a><a class="headerlink" href="#native-contacts-analysis-mdanalysis-analysis-contacts" title="Permalink to this headline">¶</a></h1>
+<h1>3.1.2. Native contacts analysis &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.contacts" title="MDAnalysis.analysis.contacts"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></code></a><a class="headerlink" href="#native-contacts-analysis-mdanalysis-analysis-contacts" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -134,19 +134,19 @@ <h1>3.1.2. Native contacts analysis &#8212; <a class="reference internal" href="
 analysis:</p>
 <ol class="arabic simple">
 <li>Contacts between two groups of atoms are defined with
-<a class="reference internal" href="#MDAnalysis.analysis.contacts.ContactAnalysis1" title="MDAnalysis.analysis.contacts.ContactAnalysis1"><tt class="xref py py-class docutils literal"><span class="pre">ContactAnalysis1</span></tt></a>), which allows one to calculate <em>q(t)</em> over
+<a class="reference internal" href="#MDAnalysis.analysis.contacts.ContactAnalysis1" title="MDAnalysis.analysis.contacts.ContactAnalysis1"><code class="xref py py-class docutils literal"><span class="pre">ContactAnalysis1</span></code></a>), which allows one to calculate <em>q(t)</em> over
 time. This is especially useful in order to look at native contacts during
 an equilibrium simulation where one can also look at the average matrix of
-native contacts (see <a class="reference internal" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.plot_qavg" title="MDAnalysis.analysis.contacts.ContactAnalysis1.plot_qavg"><tt class="xref py py-meth docutils literal"><span class="pre">ContactAnalysis1.plot_qavg()</span></tt></a>).</li>
+native contacts (see <a class="reference internal" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.plot_qavg" title="MDAnalysis.analysis.contacts.ContactAnalysis1.plot_qavg"><code class="xref py py-meth docutils literal"><span class="pre">ContactAnalysis1.plot_qavg()</span></code></a>).</li>
 <li>Contacts are defined within one group in a protein (e.g. all C-alpha atoms)
 but relative to <em>two different conformations</em> 1 and 2, using
-<a class="reference internal" href="#MDAnalysis.analysis.contacts.ContactAnalysis" title="MDAnalysis.analysis.contacts.ContactAnalysis"><tt class="xref py py-class docutils literal"><span class="pre">ContactAnalysis</span></tt></a>. This allows one to do a <em>q1-q2</em> analysis that
+<a class="reference internal" href="#MDAnalysis.analysis.contacts.ContactAnalysis" title="MDAnalysis.analysis.contacts.ContactAnalysis"><code class="xref py py-class docutils literal"><span class="pre">ContactAnalysis</span></code></a>. This allows one to do a <em>q1-q2</em> analysis that
 shows how native contacts of state 1 change in comparison to native contacts
 of state 2.  Transition pathways have been analyzed in terms of these two
 variables q1 and q2 that relate to the native contacts in the end states of
 the transition.</li>
 </ol>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">See <a class="reference external" href="http://lorentz.dynstr.pasteur.fr/joel/adenylate.php">http://lorentz.dynstr.pasteur.fr/joel/adenylate.php</a> for an
 example of contact analysis applied to MinActionPath trajectories of AdK
@@ -201,7 +201,7 @@ <h3>3.1.2.1.1. One-dimensional contact analysis<a class="headerlink" href="#one-
 matrix of all contacts, averaged over the trajectory. This plot makes
 more sense for an equilibrium trajectory than for the example above
 but is is included for illustration.</p>
-<p>See the docs for <a class="reference internal" href="#MDAnalysis.analysis.contacts.ContactAnalysis1" title="MDAnalysis.analysis.contacts.ContactAnalysis1"><tt class="xref py py-class docutils literal"><span class="pre">ContactAnalysis1</span></tt></a> for another example.</p>
+<p>See the docs for <a class="reference internal" href="#MDAnalysis.analysis.contacts.ContactAnalysis1" title="MDAnalysis.analysis.contacts.ContactAnalysis1"><code class="xref py py-class docutils literal"><span class="pre">ContactAnalysis1</span></code></a> for another example.</p>
 </div>
 <div class="section" id="two-dimensional-contact-analysis-q1-q2">
 <h3>3.1.2.1.2. Two-dimensional contact analysis (q1-q2)<a class="headerlink" href="#two-dimensional-contact-analysis-q1-q2" title="Permalink to this headline">¶</a></h3>
@@ -221,23 +221,24 @@ <h3>3.1.2.1.2. Two-dimensional contact analysis (q1-q2)<a class="headerlink" hre
 <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.contacts.</tt><tt class="descname">ContactAnalysis</tt><big>(</big><em>topology</em>, <em>trajectory</em>, <em>ref1=None</em>, <em>ref2=None</em>, <em>radius=8.0</em>, <em>targetdir='.'</em>, <em>infix=''</em>, <em>force=False</em>, <em>selection='name CA'</em>, <em>centroids=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.contacts.</code><code class="descname">ContactAnalysis</code><span class="sig-paren">(</span><em>topology</em>, <em>trajectory</em>, <em>ref1=None</em>, <em>ref2=None</em>, <em>radius=8.0</em>, <em>targetdir='.'</em>, <em>infix=''</em>, <em>force=False</em>, <em>selection='name CA'</em>, <em>centroids=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis" title="Permalink to this definition">¶</a></dt>
 <dd><p>Perform a native contact analysis (&#8220;q1-q2&#8221;).</p>
 <p>The analysis of the trajectory is performed with the
-<a class="reference internal" href="#MDAnalysis.analysis.contacts.ContactAnalysis.run" title="MDAnalysis.analysis.contacts.ContactAnalysis.run"><tt class="xref py py-meth docutils literal"><span class="pre">ContactAnalysis.run()</span></tt></a> method. The result is stored in
-<tt class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis.timeseries</span></tt>. It is a numpy array which
+<a class="reference internal" href="#MDAnalysis.analysis.contacts.ContactAnalysis.run" title="MDAnalysis.analysis.contacts.ContactAnalysis.run"><code class="xref py py-meth docutils literal"><span class="pre">ContactAnalysis.run()</span></code></a> method. The result is stored in
+<code class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis.timeseries</span></code>. It is a numpy array which
 contains the frame number at index 0, q1 and q2 at index 1 and 2,
 and the total number of contacts in 3 and 4.</p>
-<div class="highlight-python"><pre>frame  q1 q2  n1 n2</pre>
+<div class="highlight-python"><div class="highlight"><pre>frame  q1 q2  n1 n2
+</pre></div>
 </div>
 <p>The total number of contacts in the reference states 1 and 2 are
-stored in <tt class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis.nref</span></tt> (index 0 and 1).</p>
+stored in <code class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis.nref</span></code> (index 0 and 1).</p>
 <p>Calculate native contacts from two reference structures.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>topology</em></dt>
 <dd><p class="first last">psf or pdb file</p>
 </dd>
@@ -245,11 +246,11 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 <dd><p class="first last">dcd or xtc/trr file</p>
 </dd>
 <dt><em>ref1</em></dt>
-<dd><p class="first last">structure of the reference conformation 1 (pdb); if <tt class="docutils literal"><span class="pre">None</span></tt> the <em>first</em>
+<dd><p class="first last">structure of the reference conformation 1 (pdb); if <code class="docutils literal"><span class="pre">None</span></code> the <em>first</em>
 frame of the trajectory is chosen</p>
 </dd>
 <dt><em>ref2</em></dt>
-<dd><p class="first last">structure of the reference conformation 2 (pdb); if <tt class="docutils literal"><span class="pre">None</span></tt> the <em>last</em>
+<dd><p class="first last">structure of the reference conformation 2 (pdb); if <code class="docutils literal"><span class="pre">None</span></code> the <em>last</em>
 frame of the trajectory is chosen</p>
 </dd>
 <dt><em>radius</em></dt>
@@ -272,11 +273,11 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 <p class="first admonition-title">Note</p>
 <p class="last">If <em>selection</em> produces more than one atom per
 residue then you will get multiple contacts per
-residue unless you also set <em>centroids</em> = <tt class="docutils literal"><span class="pre">True</span></tt></p>
+residue unless you also set <em>centroids</em> = <code class="docutils literal"><span class="pre">True</span></code></p>
 </div>
 </dd>
 <dt><em>centroids</em></dt>
-<dd><p class="first last">If set to <tt class="docutils literal"><span class="pre">True</span></tt>, use the centroids for the selected atoms on a
+<dd><p class="first last">If set to <code class="docutils literal"><span class="pre">True</span></code>, use the centroids for the selected atoms on a
 per-residue basis to compute contacts. This allows, for instance
 defining the sidechains as <em>selection</em> and then computing distances
 between sidechain centroids.</p>
@@ -295,24 +296,24 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 <p>The timeseries is written to a bzip2-compressed file in <em>targetdir</em>
 named &#8220;basename(<em>trajectory</em>)*infix*_q1q2.dat.bz2&#8221; and is also
 accessible as the attribute
-<tt class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis.timeseries</span></tt>.</p>
+<code class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis.timeseries</span></code>.</p>
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis.get_distance_array">
-<tt class="descname">get_distance_array</tt><big>(</big><em>g</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.get_distance_array"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.get_distance_array" title="Permalink to this definition">¶</a></dt>
+<code class="descname">get_distance_array</code><span class="sig-paren">(</span><em>g</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.get_distance_array"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.get_distance_array" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate the self_distance_array for atoms in group <em>g</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>results</em></dt>
-<dd><p class="first last">passed on to <a class="reference internal" href="../lib/distances.html#MDAnalysis.lib.distances.self_distance_array" title="MDAnalysis.lib.distances.self_distance_array"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.distances.self_distance_array()</span></tt></a>
+<dd><p class="first last">passed on to <a class="reference internal" href="../lib/distances.html#MDAnalysis.lib.distances.self_distance_array" title="MDAnalysis.lib.distances.self_distance_array"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.distances.self_distance_array()</span></code></a>
 as a preallocated array</p>
 </dd>
 <dt><em>centroids</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: calculate per-residue centroids from the selected atoms;
-<tt class="docutils literal"><span class="pre">False</span></tt>: consider each atom separately; <tt class="docutils literal"><span class="pre">None</span></tt>: use the class
-default for <em>centroids</em> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: calculate per-residue centroids from the selected atoms;
+<code class="docutils literal"><span class="pre">False</span></code>: consider each atom separately; <code class="docutils literal"><span class="pre">None</span></code>: use the class
+default for <em>centroids</em> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -323,26 +324,26 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis.load">
-<tt class="descname">load</tt><big>(</big><em>filename</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.load"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.load" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.load"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.load" title="Permalink to this definition">¶</a></dt>
 <dd><p>Load the data file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis.output_exists">
-<tt class="descname">output_exists</tt><big>(</big><em>force=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.output_exists"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.output_exists" title="Permalink to this definition">¶</a></dt>
+<code class="descname">output_exists</code><span class="sig-paren">(</span><em>force=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.output_exists"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.output_exists" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return True if default output file already exists.</p>
 <p>Disable with force=True (will always return False)</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis.plot">
-<tt class="descname">plot</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.plot" title="Permalink to this definition">¶</a></dt>
+<code class="descname">plot</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.plot" title="Permalink to this definition">¶</a></dt>
 <dd><p>Plot q1-q2.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis.qN">
-<tt class="descname">qN</tt><big>(</big><em>q</em>, <em>n</em>, <em>out=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.qN"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.qN" title="Permalink to this definition">¶</a></dt>
+<code class="descname">qN</code><span class="sig-paren">(</span><em>q</em>, <em>n</em>, <em>out=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.qN"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.qN" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate native contacts relative to state n.</p>
 <p>If <em>out</em> is supplied as a pre-allocated array of the correct
 shape then it is filled instead of allocating a new one in
@@ -351,7 +352,7 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis.qarray">
-<tt class="descname">qarray</tt><big>(</big><em>d</em>, <em>out=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.qarray"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.qarray" title="Permalink to this definition">¶</a></dt>
+<code class="descname">qarray</code><span class="sig-paren">(</span><em>d</em>, <em>out=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.qarray"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.qarray" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return distance array with True for contacts.</p>
 <p>If <em>out</em> is supplied as a pre-allocated array of the correct
 shape then it is filled instead of allocating a new one in
@@ -360,9 +361,9 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis.run">
-<tt class="descname">run</tt><big>(</big><em>store=True</em>, <em>force=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>store=True</em>, <em>force=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Analyze trajectory and produce timeseries.</p>
-<p>Stores results in <tt class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis.timeseries</span></tt> (if
+<p>Stores results in <code class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis.timeseries</span></code> (if
 store=True) and writes them to a bzip2-compressed data file.</p>
 </dd></dl>
 
@@ -370,16 +371,16 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis1">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.contacts.</tt><tt class="descname">ContactAnalysis1</tt><big>(</big><em>*args</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.contacts.</code><code class="descname">ContactAnalysis1</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1" title="Permalink to this definition">¶</a></dt>
 <dd><p>Perform a very flexible native contact analysis with respect to a single reference.</p>
 <dl class="class">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis1.ContactAnalysis1">
-<em class="property">class </em><tt class="descname">ContactAnalysis1</tt><big>(</big><em>topology</em>, <em>trajectory</em><span class="optional">[</span>, <em>selection</em><span class="optional">[</span>, <em>refgroup</em><span class="optional">[</span>, <em>radius</em><span class="optional">[</span>, <em>outfile</em><span class="optional">]</span><span class="optional">]</span><span class="optional">]</span><span class="optional">]</span><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.ContactAnalysis1" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descname">ContactAnalysis1</code><span class="sig-paren">(</span><em>topology</em>, <em>trajectory</em><span class="optional">[</span>, <em>selection</em><span class="optional">[</span>, <em>refgroup</em><span class="optional">[</span>, <em>radius</em><span class="optional">[</span>, <em>outfile</em><span class="optional">]</span><span class="optional">]</span><span class="optional">]</span><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.ContactAnalysis1" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="class">
 <dt>
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.contacts.</tt><tt class="descname">ContactAnalysis1</tt><big>(</big><em>universe</em><span class="optional">[</span>, <em>selection</em><span class="optional">[</span>, <em>refgroup</em><span class="optional">[</span>, <em>radius</em><span class="optional">[</span>, <em>outfile</em><span class="optional">]</span><span class="optional">]</span><span class="optional">]</span><span class="optional">]</span><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1"><span class="viewcode-link">[source]</span></a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.contacts.</code><code class="descname">ContactAnalysis1</code><span class="sig-paren">(</span><em>universe</em><span class="optional">[</span>, <em>selection</em><span class="optional">[</span>, <em>refgroup</em><span class="optional">[</span>, <em>radius</em><span class="optional">[</span>, <em>outfile</em><span class="optional">]</span><span class="optional">]</span><span class="optional">]</span><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1"><span class="viewcode-link">[source]</span></a></dt>
 <dd></dd></dl>
 
 <p>This analysis class allows one to calculate the fraction of native contacts
@@ -388,7 +389,7 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 structure of a complex, and as the two groups atoms one selects two
 molecules A and B in the complex. Then the question to be answered by <em>q</em>
 is, is which percentage of the contacts between A and B persist during the simulation.</p>
-<p>First prepare <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> selections for
+<p>First prepare <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> selections for
 the reference atoms; this example uses some arbitrary selections:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">ref</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="s">&#39;crystal.pdb&#39;</span><span class="p">)</span>
 <span class="n">refA</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&#39;name CA and segid A and resid 6:100&#39;</span><span class="p">)</span>
@@ -400,9 +401,9 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </pre></div>
 </div>
 <p>We then need two selection strings <em>selA</em> and <em>selB</em> that, when applied as
-<tt class="docutils literal"><span class="pre">u.select_atoms(selA)</span></tt> produce a list of atoms that is equivalent to the
-reference (i.e. <tt class="docutils literal"><span class="pre">u.select_atoms(selA)</span></tt> must select the same atoms as
-<tt class="docutils literal"><span class="pre">refA</span></tt> in this example):</p>
+<code class="docutils literal"><span class="pre">u.select_atoms(selA)</span></code> produce a list of atoms that is equivalent to the
+reference (i.e. <code class="docutils literal"><span class="pre">u.select_atoms(selA)</span></code> must select the same atoms as
+<code class="docutils literal"><span class="pre">refA</span></code> in this example):</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">selA</span> <span class="o">=</span> <span class="s">&#39;name CA and resid 1:95&#39;</span>     <span class="c"># corresponds to refA</span>
 <span class="n">selB</span> <span class="o">=</span> <span class="s">&#39;name CA and resid 150:189&#39;</span>  <span class="c"># corresponds to refB</span>
 </pre></div>
@@ -417,12 +418,12 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 <div class="highlight-python"><div class="highlight"><pre><span class="n">CA1</span> <span class="o">=</span> <span class="n">ContactAnalysis1</span><span class="p">(</span><span class="n">u</span><span class="p">,</span> <span class="n">selection</span><span class="o">=</span><span class="p">(</span><span class="n">selA</span><span class="p">,</span><span class="n">selB</span><span class="p">),</span> <span class="n">refgroup</span><span class="o">=</span><span class="p">(</span><span class="n">refA</span><span class="p">,</span><span class="n">refB</span><span class="p">),</span> <span class="n">radius</span><span class="o">=</span><span class="mf">8.0</span><span class="p">,</span> <span class="n">outfile</span><span class="o">=</span><span class="s">&quot;q.dat&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>If the groups do not match in length then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
+<p>If the groups do not match in length then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
 <p>The analysis across the whole trajectory is performed with</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">CA1</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
 </pre></div>
 </div>
-<p>Results are saved to <em>outfile</em> (<tt class="docutils literal"><span class="pre">framenumber</span> <span class="pre">q</span> <span class="pre">N</span></tt> per line) and
+<p>Results are saved to <em>outfile</em> (<code class="docutils literal"><span class="pre">framenumber</span> <span class="pre">q</span> <span class="pre">N</span></code> per line) and
 can also be plotted with</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">CA1</span><span class="o">.</span><span class="n">plot</span><span class="p">()</span>        <span class="c"># plots the time series q(t)</span>
 <span class="n">CA1</span><span class="o">.</span><span class="n">plot_qavg</span><span class="p">()</span>   <span class="c"># plots the matrix of average contacts &lt;q&gt;</span>
@@ -440,7 +441,7 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>topology</em></dt>
 <dd><p class="first last">psf or pdb file</p>
 </dd>
@@ -449,19 +450,19 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </dd>
 <dt><em>universe</em></dt>
 <dd><p class="first last">instead of a topology/trajectory combination, one can also supply
-a <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt></p>
+a <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code></p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>selection</em></dt>
 <dd><p class="first last">selection string that determines which distances are calculated; if this
 is a tuple or list with two entries then distances are calculated between
 these two different groups [&#8220;name CA or name B*&#8221;]</p>
 </dd>
 <dt><em>refgroup</em></dt>
-<dd><p class="first last">reference group, either a single <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
+<dd><p class="first last">reference group, either a single <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
 (if there is only a single <em>selection</em>) or a list of two such groups.
 The reference contacts are directly computed from <em>refgroup</em> and hence
 the atoms in the reference group(s) must be equivalent to the ones produced
@@ -477,7 +478,7 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 default name &#8220;q1.dat.gz&#8221; the &lt;q&gt; file will be &#8220;q1.array.gz&#8221;. The
 format is the matrix in column-row format, i.e. selection 1
 residues are the columns and selection 2 residues are rows. The
-file can be read with <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.loadtxt.html#numpy.loadtxt" title="(in NumPy v1.9)"><tt class="xref py py-func docutils literal"><span class="pre">numpy.loadtxt()</span></tt></a>.  [&#8220;q1.dat.gz&#8221;]</p>
+file can be read with <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.loadtxt.html#numpy.loadtxt" title="(in NumPy v1.9)"><code class="xref py py-func docutils literal"><span class="pre">numpy.loadtxt()</span></code></a>.  [&#8220;q1.dat.gz&#8221;]</p>
 </dd>
 </dl>
 </td>
@@ -490,53 +491,53 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 relative to the reference state 1 (typically the starting conformation
 of the trajectory).</p>
 <p>The timeseries is written to a file <em>outfile</em> and is also accessible as
-the attribute <tt class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis1.timeseries</span></tt>.</p>
+the attribute <code class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis1.timeseries</span></code>.</p>
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis1.load">
-<tt class="descclassname">ContactAnalysis1.</tt><tt class="descname">load</tt><big>(</big><em>filename</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.load"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.load" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">ContactAnalysis1.</code><code class="descname">load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.load"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.load" title="Permalink to this definition">¶</a></dt>
 <dd><p>Load the data file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis1.output_exists">
-<tt class="descclassname">ContactAnalysis1.</tt><tt class="descname">output_exists</tt><big>(</big><em>force=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.output_exists"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.output_exists" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">ContactAnalysis1.</code><code class="descname">output_exists</code><span class="sig-paren">(</span><em>force=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.output_exists"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.output_exists" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return True if default output file already exists.</p>
 <p>Disable with force=True (will always return False)</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis1.plot">
-<tt class="descclassname">ContactAnalysis1.</tt><tt class="descname">plot</tt><big>(</big><em>filename=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.plot" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">ContactAnalysis1.</code><code class="descname">plot</code><span class="sig-paren">(</span><em>filename=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.plot" title="Permalink to this definition">¶</a></dt>
 <dd><p>Plot q(t).</p>
 <dl class="function">
 <dt>
-<tt class="descname">plot</tt><big>(</big><span class="optional">[</span><em>filename</em>, <em>...</em><span class="optional">]</span><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.plot"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">plot</code><span class="sig-paren">(</span><span class="optional">[</span><em>filename</em>, <em>...</em><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.plot"><span class="viewcode-link">[source]</span></a></dt>
 <dd></dd></dl>
 
 <p>If <em>filename</em> is supplied then the figure is also written to file (the
 suffix determines the file type, e.g. pdf, png, eps, ...). All other
-keyword arguments are passed on to <tt class="xref py py-func docutils literal"><span class="pre">pylab.plot()</span></tt>.</p>
+keyword arguments are passed on to <code class="xref py py-func docutils literal"><span class="pre">pylab.plot()</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis1.plot_qavg">
-<tt class="descclassname">ContactAnalysis1.</tt><tt class="descname">plot_qavg</tt><big>(</big><em>filename=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.plot_qavg"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.plot_qavg" title="Permalink to this definition">¶</a></dt>
-<dd><p>Plot <tt class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis1.qavg</span></tt>, the matrix of average native contacts.</p>
+<code class="descclassname">ContactAnalysis1.</code><code class="descname">plot_qavg</code><span class="sig-paren">(</span><em>filename=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.plot_qavg"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.plot_qavg" title="Permalink to this definition">¶</a></dt>
+<dd><p>Plot <code class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis1.qavg</span></code>, the matrix of average native contacts.</p>
 <dl class="function">
 <dt>
-<tt class="descname">plot_qavg</tt><big>(</big><span class="optional">[</span><em>filename</em>, <em>...</em><span class="optional">]</span><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.plot_qavg"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">plot_qavg</code><span class="sig-paren">(</span><span class="optional">[</span><em>filename</em>, <em>...</em><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.plot_qavg"><span class="viewcode-link">[source]</span></a></dt>
 <dd></dd></dl>
 
 <p>If <em>filename</em> is supplied then the figure is also written to file (the
 suffix determines the file type, e.g. pdf, png, eps, ...). All other
-keyword arguments are passed on to <tt class="xref py py-func docutils literal"><span class="pre">pylab.imshow()</span></tt>.</p>
+keyword arguments are passed on to <code class="xref py py-func docutils literal"><span class="pre">pylab.imshow()</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis1.qN">
-<tt class="descclassname">ContactAnalysis1.</tt><tt class="descname">qN</tt><big>(</big><em>q</em>, <em>out=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.qN"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.qN" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">ContactAnalysis1.</code><code class="descname">qN</code><span class="sig-paren">(</span><em>q</em>, <em>out=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.qN"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.qN" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate native contacts relative to reference state.</p>
-<p><em>q</em> is the matrix of contacts (e.g. <tt class="xref py py-attr docutils literal"><span class="pre">q</span></tt>).</p>
+<p><em>q</em> is the matrix of contacts (e.g. <code class="xref py py-attr docutils literal"><span class="pre">q</span></code>).</p>
 <p>If <em>out</em> is supplied as a pre-allocated array of the correct
 shape then it is filled instead of allocating a new one in
 order to increase performance.</p>
@@ -545,10 +546,10 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis1.qarray">
-<tt class="descclassname">ContactAnalysis1.</tt><tt class="descname">qarray</tt><big>(</big><em>d</em>, <em>out=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.qarray"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.qarray" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">ContactAnalysis1.</code><code class="descname">qarray</code><span class="sig-paren">(</span><em>d</em>, <em>out=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.qarray"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.qarray" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return distance array with True for contacts.</p>
 <p><em>d</em> is the matrix of distances. The method uses the value of
-<tt class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis1.radius</span></tt> to determine if a <tt class="docutils literal"><span class="pre">distance</span> <span class="pre">&lt;</span> <span class="pre">radius</span></tt>
+<code class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis1.radius</span></code> to determine if a <code class="docutils literal"><span class="pre">distance</span> <span class="pre">&lt;</span> <span class="pre">radius</span></code>
 is considered a contact.</p>
 <p>If <em>out</em> is supplied as a pre-allocated array of the correct
 shape then it is filled instead of allocating a new one in
@@ -558,9 +559,9 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.contacts.ContactAnalysis1.run">
-<tt class="descclassname">ContactAnalysis1.</tt><tt class="descname">run</tt><big>(</big><em>store=True</em>, <em>force=False</em>, <em>start_frame=1</em>, <em>end_frame=None</em>, <em>step_value=1</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.run" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">ContactAnalysis1.</code><code class="descname">run</code><span class="sig-paren">(</span><em>store=True</em>, <em>force=False</em>, <em>start_frame=1</em>, <em>end_frame=None</em>, <em>step_value=1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#ContactAnalysis1.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.ContactAnalysis1.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Analyze trajectory and produce timeseries.</p>
-<p>Stores results in <tt class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis1.timeseries</span></tt> (if store=True)
+<p>Stores results in <code class="xref py py-attr docutils literal"><span class="pre">ContactAnalysis1.timeseries</span></code> (if store=True)
 and writes them to a data file. The average q is written to a second
 data file.
 <em>start_frame</em></p>
@@ -585,7 +586,7 @@ <h2>3.1.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -600,11 +601,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="align.html" title="3.1.1. Coordinate fitting and alignment — MDAnalysis.analysis.align"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -614,7 +615,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/density.html b/package/doc/html/documentation_pages/analysis/density.html
index d0e6ff270b3..2ce3fbee60b 100644
--- a/package/doc/html/documentation_pages/analysis/density.html
+++ b/package/doc/html/documentation_pages/analysis/density.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.6.1. Generating densities from trajectories — MDAnalysis.analysis.density &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.6.1. Generating densities from trajectories — MDAnalysis.analysis.density &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="3.6.2. Water dynamics analysis — MDAnalysis.analysis.waterdynamics" href="waterdynamics.html" />
     <link rel="prev" title="3.5.2. HELANAL — analysis of protein helices" href="helanal.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="helanal.html" title="3.5.2. HELANAL — analysis of protein helices"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.6.1. Generating densities from trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.density</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.6.1. Generating densities from trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.density</span></code></a><ul>
 <li><a class="reference internal" href="#generating-a-density-from-a-md-trajectory">3.6.1.1. Generating a density from a MD trajectory</a></li>
 <li><a class="reference internal" href="#classes-and-functions">3.6.1.2. Classes and Functions</a></li>
 </ul>
@@ -74,13 +72,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">3.5.2. HELANAL &#8212; analysis of protein helices</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="waterdynamics.html"
-                        title="next chapter">3.6.2. Water dynamics analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/analysis/density.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">3.6.2. Water dynamics analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/analysis/density.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -99,10 +99,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.density"></span><div class="section" id="generating-densities-from-trajectories-mdanalysis-analysis-density">
-<h1>3.6.1. Generating densities from trajectories &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.density" title="MDAnalysis.analysis.density"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.density</span></tt></a><a class="headerlink" href="#generating-densities-from-trajectories-mdanalysis-analysis-density" title="Permalink to this headline">¶</a></h1>
+<h1>3.6.1. Generating densities from trajectories &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.density" title="MDAnalysis.analysis.density"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.density</span></code></a><a class="headerlink" href="#generating-densities-from-trajectories-mdanalysis-analysis-density" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -138,38 +138,38 @@ <h2>3.6.1.1. Generating a density from a MD trajectory<a class="headerlink" href
 </div>
 <p>The positions of all water oxygens are histogrammed on a grid with spacing
 <em>delta</em> = 1 A. Initially the density is measured in 1/A**3. With the
-<a class="reference internal" href="#MDAnalysis.analysis.density.Density.convert_density" title="MDAnalysis.analysis.density.Density.convert_density"><tt class="xref py py-meth docutils literal"><span class="pre">Density.convert_density()</span></tt></a> method, the units of measurement are
+<a class="reference internal" href="#MDAnalysis.analysis.density.Density.convert_density" title="MDAnalysis.analysis.density.Density.convert_density"><code class="xref py py-meth docutils literal"><span class="pre">Density.convert_density()</span></code></a> method, the units of measurement are
 changed. In the example we are now measuring the density relative to the
 literature value of the TIP3P water model at ambient conditions (see the values
-in <a class="reference internal" href="../units.html#MDAnalysis.units.water" title="MDAnalysis.units.water"><tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.units.water</span></tt></a> for details). Finally, the density is
+in <a class="reference internal" href="../units.html#MDAnalysis.units.water" title="MDAnalysis.units.water"><code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.units.water</span></code></a> for details). Finally, the density is
 writte as an <a class="reference external" href="http://www.opendx.org/">OpenDX</a> compatible file that can be read in <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a> or <a class="reference external" href="http://www.pymol.org/">PyMOL</a>.</p>
-<p>See <a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><tt class="xref py py-class docutils literal"><span class="pre">Density</span></tt></a> for details. In particular, the density is stored
-as a NumPy array in <tt class="xref py py-attr docutils literal"><span class="pre">Density.grid</span></tt>, which can be processed in
+<p>See <a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><code class="xref py py-class docutils literal"><span class="pre">Density</span></code></a> for details. In particular, the density is stored
+as a NumPy array in <code class="xref py py-attr docutils literal"><span class="pre">Density.grid</span></code>, which can be processed in
 any manner.</p>
 </div>
 <div class="section" id="classes-and-functions">
 <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-functions" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.analysis.density.Density">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.density.</tt><tt class="descname">Density</tt><big>(</big><em>*args</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#Density"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.Density" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">gridData.core.Grid</span></tt></p>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.density.</code><code class="descname">Density</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#Density"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.Density" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">gridData.core.Grid</span></code></p>
 <p>Class representing a density on a regular cartesian grid.</p>
-<p>The data (<tt class="xref py py-attr docutils literal"><span class="pre">Density.grid</span></tt>) can be manipulated as a standard numpy
-array. Changes can be saved to a file using the <a class="reference internal" href="#MDAnalysis.analysis.density.Density.save" title="MDAnalysis.analysis.density.Density.save"><tt class="xref py py-meth docutils literal"><span class="pre">Density.save()</span></tt></a> method. The
-grid can be restored using the <a class="reference internal" href="#MDAnalysis.analysis.density.Density.load" title="MDAnalysis.analysis.density.Density.load"><tt class="xref py py-meth docutils literal"><span class="pre">Density.load()</span></tt></a> method or by supplying the
+<p>The data (<code class="xref py py-attr docutils literal"><span class="pre">Density.grid</span></code>) can be manipulated as a standard numpy
+array. Changes can be saved to a file using the <a class="reference internal" href="#MDAnalysis.analysis.density.Density.save" title="MDAnalysis.analysis.density.Density.save"><code class="xref py py-meth docutils literal"><span class="pre">Density.save()</span></code></a> method. The
+grid can be restored using the <a class="reference internal" href="#MDAnalysis.analysis.density.Density.load" title="MDAnalysis.analysis.density.Density.load"><code class="xref py py-meth docutils literal"><span class="pre">Density.load()</span></code></a> method or by supplying the
 filename to the constructor.</p>
-<p>The attribute <tt class="xref py py-attr docutils literal"><span class="pre">Density.metadata</span></tt> holds a user-defined dictionary that
-can be used to annotate the data. It is also saved with <a class="reference internal" href="#MDAnalysis.analysis.density.Density.save" title="MDAnalysis.analysis.density.Density.save"><tt class="xref py py-meth docutils literal"><span class="pre">Density.save()</span></tt></a>.</p>
-<p>The <a class="reference internal" href="#MDAnalysis.analysis.density.Density.export" title="MDAnalysis.analysis.density.Density.export"><tt class="xref py py-meth docutils literal"><span class="pre">Density.export()</span></tt></a> method always exports a 3D object
+<p>The attribute <code class="xref py py-attr docutils literal"><span class="pre">Density.metadata</span></code> holds a user-defined dictionary that
+can be used to annotate the data. It is also saved with <a class="reference internal" href="#MDAnalysis.analysis.density.Density.save" title="MDAnalysis.analysis.density.Density.save"><code class="xref py py-meth docutils literal"><span class="pre">Density.save()</span></code></a>.</p>
+<p>The <a class="reference internal" href="#MDAnalysis.analysis.density.Density.export" title="MDAnalysis.analysis.density.Density.export"><code class="xref py py-meth docutils literal"><span class="pre">Density.export()</span></code></a> method always exports a 3D object
 (written in such a way to be readable in <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a> and <a class="reference external" href="http://www.pymol.org/">PyMOL</a>), the
 rest should work for an array of any dimension.</p>
 <p>If the input histogram consists of counts per cell then the
-<a class="reference internal" href="#MDAnalysis.analysis.density.Density.make_density" title="MDAnalysis.analysis.density.Density.make_density"><tt class="xref py py-meth docutils literal"><span class="pre">Density.make_density()</span></tt></a> method converts the grid to a physical density. For
-a probability density, divide it by <tt class="xref py py-meth docutils literal"><span class="pre">Density.grid.sum()</span></tt> or use <tt class="docutils literal"><span class="pre">normed=True</span></tt>
-right away in <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.histogramdd.html#numpy.histogramdd" title="(in NumPy v1.9)"><tt class="xref py py-func docutils literal"><span class="pre">histogramdd()</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.analysis.density.Density.make_density" title="MDAnalysis.analysis.density.Density.make_density"><code class="xref py py-meth docutils literal"><span class="pre">Density.make_density()</span></code></a> method converts the grid to a physical density. For
+a probability density, divide it by <code class="xref py py-meth docutils literal"><span class="pre">Density.grid.sum()</span></code> or use <code class="docutils literal"><span class="pre">normed=True</span></code>
+right away in <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.histogramdd.html#numpy.histogramdd" title="(in NumPy v1.9)"><code class="xref py py-func docutils literal"><span class="pre">histogramdd()</span></code></a>.</p>
 <p>The user <em>should</em> set the <em>parameters</em> keyword (see docs for the
 constructor); in particular, if the data are already a density, one must
-set <em>isDensity</em> == <tt class="docutils literal"><span class="pre">True</span></tt> because there is no reliable way to detect if
+set <em>isDensity</em> == <code class="docutils literal"><span class="pre">True</span></code> because there is no reliable way to detect if
 data represent counts or a density. As a special convenience, if data are
 read from a file and the user has not set <em>isDensity</em> then it is assumed
 that the data are in fact a density.</p>
@@ -203,51 +203,51 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <span class="n">D</span><span class="o">.</span><span class="n">convert_density</span><span class="p">(</span><span class="s">&#39;water&#39;</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>After the final step, <tt class="docutils literal"><span class="pre">D</span></tt> will contain a density on a grid measured in
+<p>After the final step, <code class="docutils literal"><span class="pre">D</span></code> will contain a density on a grid measured in
 Angstrom, with the density values itself measured relative to the
 density of water.</p>
 </li>
 </ol>
-<p><a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><tt class="xref py py-class docutils literal"><span class="pre">Density</span></tt></a> objects can be algebraically manipulated (added,
+<p><a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><code class="xref py py-class docutils literal"><span class="pre">Density</span></code></a> objects can be algebraically manipulated (added,
 subtracted, multiplied, ...)  but there are <em>no sanity checks</em> in place to
 make sure that units, metadata, etc are compatible!</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">It is suggested to construct the Grid object from a histogram,
 to supply the appropriate length unit, and to use
-<a class="reference internal" href="#MDAnalysis.analysis.density.Density.make_density" title="MDAnalysis.analysis.density.Density.make_density"><tt class="xref py py-meth docutils literal"><span class="pre">Density.make_density()</span></tt></a> to obtain a density. This ensures
+<a class="reference internal" href="#MDAnalysis.analysis.density.Density.make_density" title="MDAnalysis.analysis.density.Density.make_density"><code class="xref py py-meth docutils literal"><span class="pre">Density.make_density()</span></code></a> to obtain a density. This ensures
 that the length- and the density unit correspond to each other.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.analysis.density.Grid" title="MDAnalysis.analysis.density.Grid"><tt class="xref py py-class docutils literal"><span class="pre">Grid</span></tt></a> which is the base class of
-<a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><tt class="xref py py-class docutils literal"><span class="pre">Density</span></tt></a>. (<a class="reference internal" href="#MDAnalysis.analysis.density.Grid" title="MDAnalysis.analysis.density.Grid"><tt class="xref py py-class docutils literal"><span class="pre">Grid</span></tt></a> has been imported from
-<tt class="xref py py-class docutils literal"><span class="pre">gridData.Grid</span></tt> which is part of <a class="reference external" href="https://github.com/orbeckst/GridDataFormats">GridDataFormats</a>).</p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.analysis.density.Grid" title="MDAnalysis.analysis.density.Grid"><code class="xref py py-class docutils literal"><span class="pre">Grid</span></code></a> which is the base class of
+<a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><code class="xref py py-class docutils literal"><span class="pre">Density</span></code></a>. (<a class="reference internal" href="#MDAnalysis.analysis.density.Grid" title="MDAnalysis.analysis.density.Grid"><code class="xref py py-class docutils literal"><span class="pre">Grid</span></code></a> has been imported from
+<code class="xref py py-class docutils literal"><span class="pre">gridData.Grid</span></code> which is part of <a class="reference external" href="https://github.com/orbeckst/GridDataFormats">GridDataFormats</a>).</p>
 </div>
-<p>Create a <a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><tt class="xref py py-class docutils literal"><span class="pre">Density</span></tt></a> from data.</p>
+<p>Create a <a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><code class="xref py py-class docutils literal"><span class="pre">Density</span></code></a> from data.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>grid</em></dt>
-<dd><p class="first last">histogram or density, typically a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a></p>
+<dd><p class="first last">histogram or density, typically a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a></p>
 </dd>
 <dt><em>edges</em></dt>
 <dd><p class="first last">list of arrays, the lower and upper bin edges along the axes</p>
 </dd>
 <dt><em>parameters</em></dt>
 <dd><p class="first">dictionary of class parameters; saved with
-<a class="reference internal" href="#MDAnalysis.analysis.density.Density.save" title="MDAnalysis.analysis.density.Density.save"><tt class="xref py py-meth docutils literal"><span class="pre">Density.save()</span></tt></a>. The following keys are meaningful to
+<a class="reference internal" href="#MDAnalysis.analysis.density.Density.save" title="MDAnalysis.analysis.density.Density.save"><code class="xref py py-meth docutils literal"><span class="pre">Density.save()</span></code></a>. The following keys are meaningful to
 the class. Meaning of the values are listed:</p>
 <blockquote class="last">
 <div><p><em>isDensity</em></p>
 <blockquote>
 <div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">False</span></tt>: grid is a histogram with counts [default]</li>
-<li><tt class="docutils literal"><span class="pre">True</span></tt>: a density</li>
+<li><code class="docutils literal"><span class="pre">False</span></code>: grid is a histogram with counts [default]</li>
+<li><code class="docutils literal"><span class="pre">True</span></code>: a density</li>
 </ul>
-<p>Applying <tt class="xref py py-meth docutils literal"><span class="pre">Density.make_density`()</span></tt> sets it to <tt class="docutils literal"><span class="pre">True</span></tt>.</p>
+<p>Applying <code class="xref py py-meth docutils literal"><span class="pre">Density.make_density`()</span></code> sets it to <code class="docutils literal"><span class="pre">True</span></code>.</p>
 </div></blockquote>
 </div></blockquote>
 </dd>
@@ -255,16 +255,16 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <dd><p class="first">A dict with the keys</p>
 <ul class="simple">
 <li><em>length</em>:  physical unit of grid edges (Angstrom or nm) [Angstrom]</li>
-<li><em>density</em>: unit of the density if <tt class="docutils literal"><span class="pre">isDensity</span> <span class="pre">==</span> <span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">None</span></tt>
+<li><em>density</em>: unit of the density if <code class="docutils literal"><span class="pre">isDensity</span> <span class="pre">==</span> <span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">None</span></code>
 otherwise; the default is &#8220;Angstrom^{-3}&#8221; for densities (meaning A^-3).</li>
 </ul>
 <p class="last">(Actually, the default unit is the value of
-<tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.flags['length_unit']</span></tt>; in most cases this is &#8220;Angstrom&#8221;.)</p>
+<code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.flags['length_unit']</span></code>; in most cases this is &#8220;Angstrom&#8221;.)</p>
 </dd>
 <dt><em>metadata</em></dt>
 <dd><p class="first last">a user defined dictionary of arbitrary values associated with the
-density; the class does not touch <tt class="xref py py-attr docutils literal"><span class="pre">Density.metadata</span></tt> but
-stores it with <a class="reference internal" href="#MDAnalysis.analysis.density.Density.save" title="MDAnalysis.analysis.density.Density.save"><tt class="xref py py-meth docutils literal"><span class="pre">Density.save()</span></tt></a></p>
+density; the class does not touch <code class="xref py py-attr docutils literal"><span class="pre">Density.metadata</span></code> but
+stores it with <a class="reference internal" href="#MDAnalysis.analysis.density.Density.save" title="MDAnalysis.analysis.density.Density.save"><code class="xref py py-meth docutils literal"><span class="pre">Density.save()</span></code></a></p>
 </dd>
 </dl>
 </td>
@@ -273,13 +273,13 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 </table>
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Density.centers">
-<tt class="descname">centers</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Density.centers" title="Permalink to this definition">¶</a></dt>
+<code class="descname">centers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Density.centers" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns the coordinates of the centers of all grid cells as an iterator.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Density.check_compatible">
-<tt class="descname">check_compatible</tt><big>(</big><em>other</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Density.check_compatible" title="Permalink to this definition">¶</a></dt>
+<code class="descname">check_compatible</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Density.check_compatible" title="Permalink to this definition">¶</a></dt>
 <dd><p>Check if <em>other</em> can be used in an arithmetic operation.</p>
 <ol class="arabic simple">
 <li><em>other</em> is a scalar</li>
@@ -289,7 +289,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><tt class="xref py py-exc docutils literal"><span class="pre">TypeError</span></tt> if not compatible.</td>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">TypeError</span></code> if not compatible.</td>
 </tr>
 </tbody>
 </table>
@@ -297,7 +297,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Density.convert_density">
-<tt class="descname">convert_density</tt><big>(</big><em>unit='Angstrom'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#Density.convert_density"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.Density.convert_density" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_density</code><span class="sig-paren">(</span><em>unit='Angstrom'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#Density.convert_density"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.Density.convert_density" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert the density to the physical units given by <em>unit</em>.</p>
 <blockquote>
 <div>Grid.convert_to(unit)</div></blockquote>
@@ -323,10 +323,10 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <td>density of SPC water at standard conditions</td>
 </tr>
 <tr class="row-odd"><td>TIP3P</td>
-<td>... see <a class="reference internal" href="../units.html#MDAnalysis.units.water" title="MDAnalysis.units.water"><tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.units.water</span></tt></a></td>
+<td>... see <a class="reference internal" href="../units.html#MDAnalysis.units.water" title="MDAnalysis.units.water"><code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.units.water</span></code></a></td>
 </tr>
 <tr class="row-even"><td>TIP4P</td>
-<td>... see <a class="reference internal" href="../units.html#MDAnalysis.units.water" title="MDAnalysis.units.water"><tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.units.water</span></tt></a></td>
+<td>... see <a class="reference internal" href="../units.html#MDAnalysis.units.water" title="MDAnalysis.units.water"><code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.units.water</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>water</td>
 <td>density of real water at standard conditions (0.997 g/cm**3)</td>
@@ -344,12 +344,12 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 and floating point artifacts for multiple conversions.</li>
 </ol>
 </div></blockquote>
-<p>There may be some undesirable cross-interactions with <a class="reference internal" href="#MDAnalysis.analysis.density.Density.convert_length" title="MDAnalysis.analysis.density.Density.convert_length"><tt class="xref py py-meth docutils literal"><span class="pre">convert_length()</span></tt></a>...</p>
+<p>There may be some undesirable cross-interactions with <a class="reference internal" href="#MDAnalysis.analysis.density.Density.convert_length" title="MDAnalysis.analysis.density.Density.convert_length"><code class="xref py py-meth docutils literal"><span class="pre">convert_length()</span></code></a>...</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Density.convert_length">
-<tt class="descname">convert_length</tt><big>(</big><em>unit='Angstrom'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#Density.convert_length"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.Density.convert_length" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_length</code><span class="sig-paren">(</span><em>unit='Angstrom'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#Density.convert_length"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.Density.convert_length" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert Grid object to the new <em>unit</em>.</p>
 <blockquote>
 <div>Grid.convert_length(&lt;unit&gt;)</div></blockquote>
@@ -357,7 +357,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>unit</em></dt>
 <dd><p class="first last">Angstrom, nm</p>
 </dd>
@@ -370,43 +370,40 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 the user&#8217;s responsibility to supply the appropriate unit if
 the Grid object is constructed from a density. It is suggested
 to start from a histogram and a length unit and use
-<a class="reference internal" href="#MDAnalysis.analysis.density.Density.make_density" title="MDAnalysis.analysis.density.Density.make_density"><tt class="xref py py-meth docutils literal"><span class="pre">make_density()</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.analysis.density.Density.make_density" title="MDAnalysis.analysis.density.Density.make_density"><code class="xref py py-meth docutils literal"><span class="pre">make_density()</span></code></a>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Density.export">
-<tt class="descname">export</tt><big>(</big><em>filename</em>, <em>format=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Density.export" title="Permalink to this definition">¶</a></dt>
-<dd><p>export density to file using the given format.</p>
+<code class="descname">export</code><span class="sig-paren">(</span><em>filename</em>, <em>format=None</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Density.export" title="Permalink to this definition">¶</a></dt>
+<dd><p>export density to file using the given format; use &#8216;dx&#8217; for visualization.</p>
+<p>export(filename=&lt;filename&gt;,format=&lt;format&gt;)</p>
 <p>The format can also be deduced from the suffix of the filename
 though the <em>format</em> keyword takes precedence.</p>
-<p>The default format for export() is &#8216;dx&#8217;.  Use &#8216;dx&#8217; for
-visualization.</p>
-<p>Implemented formats:</p>
-<dl class="docutils">
-<dt>dx</dt>
-<dd><tt class="xref py py-mod docutils literal"><span class="pre">OpenDX</span></tt></dd>
-<dt>pickle</dt>
-<dd>pickle (use :meth:<tt class="docutils literal"><span class="pre">Grid.load`</span> <span class="pre">to</span> <span class="pre">restore);</span> <span class="pre">:meth:`Grid.save`</span>
-<span class="pre">is</span> <span class="pre">simpler</span> <span class="pre">than</span> <span class="pre">``export(format='python')</span></tt>.</dd>
-</dl>
+<p>The default format for export() is &#8216;dx&#8217;.</p>
+<p>Only implemented formats:</p>
+<p>dx        OpenDX
+pickle    pickle (use Grid.load(filename) to restore); Grid.save()</p>
+<blockquote>
+<div>is simpler than export(format=&#8217;python&#8217;).</div></blockquote>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.density.Density.interpolated">
-<tt class="descname">interpolated</tt><a class="headerlink" href="#MDAnalysis.analysis.density.Density.interpolated" title="Permalink to this definition">¶</a></dt>
+<code class="descname">interpolated</code><a class="headerlink" href="#MDAnalysis.analysis.density.Density.interpolated" title="Permalink to this definition">¶</a></dt>
 <dd><p>B-spline function over the data grid(x,y,z).</p>
 <blockquote>
 <div>interpolated([x1,x2,...],[y1,y2,...],[z1,z2,...]) -&gt; F[x1,y1,z1],F[x2,y2,z2],...</div></blockquote>
-<p>The interpolation order is set in <tt class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_spline_order</span></tt>.</p>
+<p>The interpolation order is set in <code class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_spline_order</span></code>.</p>
 <p>The interpolated function is computed once and is cached for better
-performance. Whenever <tt class="xref py py-attr docutils literal"><span class="pre">interpolation_spline_order</span></tt> is
-modified, <a class="reference internal" href="#MDAnalysis.analysis.density.Grid.interpolated" title="MDAnalysis.analysis.density.Grid.interpolated"><tt class="xref py py-meth docutils literal"><span class="pre">Grid.interpolated()</span></tt></a> is recomputed.</p>
-<p>The value for unknown data is set in <tt class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_cval</span></tt>
+performance. Whenever <code class="xref py py-attr docutils literal"><span class="pre">interpolation_spline_order</span></code> is
+modified, <a class="reference internal" href="#MDAnalysis.analysis.density.Grid.interpolated" title="MDAnalysis.analysis.density.Grid.interpolated"><code class="xref py py-meth docutils literal"><span class="pre">Grid.interpolated()</span></code></a> is recomputed.</p>
+<p>The value for unknown data is set in <code class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_cval</span></code>
 (TODO: also recompute when interpolation_cval value is changed.)</p>
 <dl class="docutils">
 <dt>Example usage for resampling::</dt>
 <dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">XX</span><span class="p">,</span><span class="n">YY</span><span class="p">,</span><span class="n">ZZ</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">mgrid</span><span class="p">[</span><span class="mi">40</span><span class="p">:</span><span class="mi">75</span><span class="p">:</span><span class="mf">0.5</span><span class="p">,</span> <span class="mi">96</span><span class="p">:</span><span class="mi">150</span><span class="p">:</span><span class="mf">0.5</span><span class="p">,</span> <span class="mi">20</span><span class="p">:</span><span class="mi">50</span><span class="p">:</span><span class="mf">0.5</span><span class="p">]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">FF</span> <span class="o">=</span> <span class="n">interpolated</span><span class="p">(</span><span class="n">XX</span><span class="p">,</span><span class="n">YY</span><span class="p">,</span><span class="n">ZZ</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">FF</span> <span class="o">=</span> <span class="n">interpolated</span><span class="p">(</span><span class="n">XX</span><span class="p">,</span><span class="n">YY</span><span class="p">,</span><span class="n">ZZ</span><span class="p">)</span>            
 </pre></div>
 </div>
 </dd>
@@ -415,7 +412,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Density.load">
-<tt class="descname">load</tt><big>(</big><em>filename</em>, <em>format=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Density.load" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load</code><span class="sig-paren">(</span><em>filename</em>, <em>format=None</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Density.load" title="Permalink to this definition">¶</a></dt>
 <dd><p>Load saved (pickled or dx) grid and edges from &lt;filename&gt;.pickle</p>
 <blockquote>
 <div>Grid.load(&lt;filename&gt;.pickle)
@@ -426,7 +423,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Density.make_density">
-<tt class="descname">make_density</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#Density.make_density"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.Density.make_density" title="Permalink to this definition">¶</a></dt>
+<code class="descname">make_density</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#Density.make_density"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.Density.make_density" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert the grid (a histogram, counts in a cell) to a density (counts/volume).</p>
 <blockquote>
 <div>make_density()</div></blockquote>
@@ -439,7 +436,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Density.resample">
-<tt class="descname">resample</tt><big>(</big><em>edges</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Density.resample" title="Permalink to this definition">¶</a></dt>
+<code class="descname">resample</code><span class="sig-paren">(</span><em>edges</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Density.resample" title="Permalink to this definition">¶</a></dt>
 <dd><p>Resample data to a new grid with edges <em>edges</em>.</p>
 <blockquote>
 <div>resample(edges) &#8211;&gt; Grid</div></blockquote>
@@ -447,18 +444,18 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <blockquote>
 <div>resample(otherGrid) &#8211;&gt; Grid</div></blockquote>
 <p>The order of the interpolation is set by
-<tt class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_spline_order</span></tt>.</p>
+<code class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_spline_order</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Density.resample_factor">
-<tt class="descname">resample_factor</tt><big>(</big><em>factor</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Density.resample_factor" title="Permalink to this definition">¶</a></dt>
+<code class="descname">resample_factor</code><span class="sig-paren">(</span><em>factor</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Density.resample_factor" title="Permalink to this definition">¶</a></dt>
 <dd><p>Resample to a new regular grid with factor*oldN cells along each dimension.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Density.save">
-<tt class="descname">save</tt><big>(</big><em>filename</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Density.save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Density.save" title="Permalink to this definition">¶</a></dt>
 <dd><p>Save a grid object to &lt;filename&gt;.pickle</p>
 <blockquote>
 <div>Grid.save(filename)</div></blockquote>
@@ -472,7 +469,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.density.density_from_Universe">
-<tt class="descclassname">MDAnalysis.analysis.density.</tt><tt class="descname">density_from_Universe</tt><big>(</big><em>universe</em>, <em>delta=1.0</em>, <em>atomselection='name OH2'</em>, <em>metadata=None</em>, <em>padding=2.0</em>, <em>cutoff=0</em>, <em>soluteselection=None</em>, <em>use_kdtree=True</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#density_from_Universe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.density_from_Universe" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.density.</code><code class="descname">density_from_Universe</code><span class="sig-paren">(</span><em>universe</em>, <em>delta=1.0</em>, <em>atomselection='name OH2'</em>, <em>metadata=None</em>, <em>padding=2.0</em>, <em>cutoff=0</em>, <em>soluteselection=None</em>, <em>use_kdtree=True</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#density_from_Universe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.density_from_Universe" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a density grid from a MDAnalysis.Universe object.</p>
 <blockquote>
 <div>density_from_Universe(universe, delta=1.0, atomselection=&#8217;name OH2&#8217;, ...) &#8211;&gt; density</div></blockquote>
@@ -480,14 +477,14 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt>universe</dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object with a trajectory</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object with a trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt>atomselection</dt>
 <dd><p class="first last">selection string (MDAnalysis syntax) for the species to be analyzed
 [&#8220;name OH2&#8221;]</p>
@@ -503,22 +500,22 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 in Angstroem [2.0]</p>
 </dd>
 <dt>soluteselection</dt>
-<dd><p class="first last">MDAnalysis selection for the solute, e.g. &#8220;protein&#8221; [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">MDAnalysis selection for the solute, e.g. &#8220;protein&#8221; [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt>cutoff</dt>
 <dd><p class="first last">With <em>cutoff</em>, select &#8216;&lt;atomsel&gt; NOT WITHIN &lt;cutoff&gt; OF &lt;soluteselection&gt;&#8217;
 (Special routines that are faster than the standard AROUND selection) [0]</p>
 </dd>
 <dt>parameters</dt>
-<dd><p class="first last">dict with some special parameters for <a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><tt class="xref py py-class docutils literal"><span class="pre">Density</span></tt></a> (see doc)</p>
+<dd><p class="first last">dict with some special parameters for <a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><code class="xref py py-class docutils literal"><span class="pre">Density</span></code></a> (see doc)</p>
 </dd>
 <dt>kwargs</dt>
-<dd><p class="first last">metadata, parameters are modified and passed on to <a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><tt class="xref py py-class docutils literal"><span class="pre">Density</span></tt></a></p>
+<dd><p class="first last">metadata, parameters are modified and passed on to <a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><code class="xref py py-class docutils literal"><span class="pre">Density</span></code></a></p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><tt class="xref py py-class docutils literal"><span class="pre">Density</span></tt></a></p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><code class="xref py py-class docutils literal"><span class="pre">Density</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -527,7 +524,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.density.density_from_trajectory">
-<tt class="descclassname">MDAnalysis.analysis.density.</tt><tt class="descname">density_from_trajectory</tt><big>(</big><em>*args</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#density_from_trajectory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.density_from_trajectory" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.density.</code><code class="descname">density_from_trajectory</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#density_from_trajectory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.density_from_trajectory" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a density grid from a trajectory.</p>
 <blockquote>
 <div>density_from_trajectory(PSF, DCD, delta=1.0, atomselection=&#8217;name OH2&#8217;, ...) &#8211;&gt; density</div></blockquote>
@@ -538,7 +535,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt>topology file</dt>
 <dd><p class="first last">any topology file understood by MDAnalysis</p>
 </dd>
@@ -550,7 +547,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt>atomselection</dt>
 <dd><p class="first last">selection string (MDAnalysis syntax) for the species to be analyzed
 [&#8220;name OH2&#8221;]</p>
@@ -566,7 +563,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 in Angstroem [2.0]</p>
 </dd>
 <dt>soluteselection</dt>
-<dd><p class="first last">MDAnalysis selection for the solute, e.g. &#8220;protein&#8221; [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">MDAnalysis selection for the solute, e.g. &#8220;protein&#8221; [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt>cutoff</dt>
 <dd><p class="first last">With <em>cutoff</em>, select &#8216;&lt;atomsel&gt; NOT WITHIN &lt;cutoff&gt; OF &lt;soluteselection&gt;&#8217;
@@ -575,20 +572,20 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><tt class="xref py py-class docutils literal"><span class="pre">Density</span></tt></a></p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><code class="xref py py-class docutils literal"><span class="pre">Density</span></code></a></p>
 </td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last">docs for <a class="reference internal" href="#MDAnalysis.analysis.density.density_from_Universe" title="MDAnalysis.analysis.density.density_from_Universe"><tt class="xref py py-func docutils literal"><span class="pre">density_from_Universe()</span></tt></a> (defaults for kwargs are defined there).</p>
+<p class="last">docs for <a class="reference internal" href="#MDAnalysis.analysis.density.density_from_Universe" title="MDAnalysis.analysis.density.density_from_Universe"><code class="xref py py-func docutils literal"><span class="pre">density_from_Universe()</span></code></a> (defaults for kwargs are defined there).</p>
 </div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.density.density_from_PDB">
-<tt class="descclassname">MDAnalysis.analysis.density.</tt><tt class="descname">density_from_PDB</tt><big>(</big><em>pdb</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#density_from_PDB"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.density_from_PDB" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.density.</code><code class="descname">density_from_PDB</code><span class="sig-paren">(</span><em>pdb</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#density_from_PDB"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.density_from_PDB" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a density from a single frame PDB.</p>
 <p>Typical use is to make a density from the crystal water
 molecules. The density is created from isotropic gaussians
@@ -596,20 +593,20 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 file then they are used to calculate the width of the gaussian.</p>
 <p>Using the <em>sigma</em> keyword, one can override this choice and
 prescribe a gaussian width for all atoms (in Angstrom), which is
-calculated as described for <a class="reference internal" href="#MDAnalysis.analysis.density.Bfactor2RMSF" title="MDAnalysis.analysis.density.Bfactor2RMSF"><tt class="xref py py-func docutils literal"><span class="pre">Bfactor2RMSF()</span></tt></a>.</p>
+calculated as described for <a class="reference internal" href="#MDAnalysis.analysis.density.Bfactor2RMSF" title="MDAnalysis.analysis.density.Bfactor2RMSF"><code class="xref py py-func docutils literal"><span class="pre">Bfactor2RMSF()</span></code></a>.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The current implementation is <em>painfully</em> slow.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.analysis.density.Bfactor2RMSF" title="MDAnalysis.analysis.density.Bfactor2RMSF"><tt class="xref py py-func docutils literal"><span class="pre">Bfactor2RMSF()</span></tt></a> and <a class="reference internal" href="#MDAnalysis.analysis.density.BfactorDensityCreator" title="MDAnalysis.analysis.density.BfactorDensityCreator"><tt class="xref py py-class docutils literal"><span class="pre">BfactorDensityCreator</span></tt></a>.</p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.analysis.density.Bfactor2RMSF" title="MDAnalysis.analysis.density.Bfactor2RMSF"><code class="xref py py-func docutils literal"><span class="pre">Bfactor2RMSF()</span></code></a> and <a class="reference internal" href="#MDAnalysis.analysis.density.BfactorDensityCreator" title="MDAnalysis.analysis.density.BfactorDensityCreator"><code class="xref py py-class docutils literal"><span class="pre">BfactorDensityCreator</span></code></a>.</p>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>pdb</em></dt>
 <dd><p class="first last">PDB file (should have the temperatureFactor set); ANISO
 records are currently <em>not</em> processed</p>
@@ -617,7 +614,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>atomselection</em></dt>
 <dd><p class="first last">selection string (MDAnalysis syntax) for the species to be analyzed
 [&#8216;resname HOH and name O&#8217;]</p>
@@ -626,19 +623,19 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <dd><p class="first last">bin size for the density grid in Angstroem (same in x,y,z) [1.0]</p>
 </dd>
 <dt><em>metadata</em></dt>
-<dd><p class="first last">dictionary of additional data to be saved with the object [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">dictionary of additional data to be saved with the object [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>padding</em></dt>
 <dd><p class="first last">increase histogram dimensions by padding (on top of initial box size) [1.0]</p>
 </dd>
 <dt><em>sigma</em></dt>
 <dd><p class="first last">width (in Angstrom) of the gaussians that are used to build up the
-density; if <tt class="docutils literal"><span class="pre">None</span></tt> then uses B-factors from <em>pdb</em> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+density; if <code class="docutils literal"><span class="pre">None</span></code> then uses B-factors from <em>pdb</em> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">a <a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><tt class="xref py py-class docutils literal"><span class="pre">Density</span></tt></a> object with a density measured relative to the
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">a <a class="reference internal" href="#MDAnalysis.analysis.density.Density" title="MDAnalysis.analysis.density.Density"><code class="xref py py-class docutils literal"><span class="pre">Density</span></code></a> object with a density measured relative to the
 water density at standard conditions</p>
 </td>
 </tr>
@@ -648,9 +645,9 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.density.Bfactor2RMSF">
-<tt class="descclassname">MDAnalysis.analysis.density.</tt><tt class="descname">Bfactor2RMSF</tt><big>(</big><em>B</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#Bfactor2RMSF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.Bfactor2RMSF" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.density.</code><code class="descname">Bfactor2RMSF</code><span class="sig-paren">(</span><em>B</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#Bfactor2RMSF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.Bfactor2RMSF" title="Permalink to this definition">¶</a></dt>
 <dd><p>Atomic root mean square fluctuation (in Angstrom) from the crystallographic B-factor</p>
-<p>RMSF and B-factor are related by <a class="reference internal" href="#willis1975">[Willis1975]</a></p>
+<p>RMSF and B-factor are related by <a class="reference internal" href="#willis1975" id="id1">[Willis1975]</a></p>
 <div class="math">
 \[B = \frac{8\pi^2}{3} \rm{RMSF}^2\]</div>
 <p>and this function returns</p>
@@ -667,7 +664,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.density.BfactorDensityCreator">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.density.</tt><tt class="descname">BfactorDensityCreator</tt><big>(</big><em>pdb</em>, <em>delta=1.0</em>, <em>atomselection='resname HOH and name O'</em>, <em>metadata=None</em>, <em>padding=1.0</em>, <em>sigma=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#BfactorDensityCreator"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.BfactorDensityCreator" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.density.</code><code class="descname">BfactorDensityCreator</code><span class="sig-paren">(</span><em>pdb</em>, <em>delta=1.0</em>, <em>atomselection='resname HOH and name O'</em>, <em>metadata=None</em>, <em>padding=1.0</em>, <em>sigma=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#BfactorDensityCreator"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.BfactorDensityCreator" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a density grid from a pdb file using MDAnalysis.</p>
 <blockquote>
 <div>dens = BfactorDensityCreator(pdb,...).Density()</div></blockquote>
@@ -678,7 +675,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 estimated by placing Gaussians of width sigma at the position of
 all selected atoms.</p>
 <p>Sigma can be fixed or taken from the B-factor field, in which case
-sigma is taken as sqrt(3.*B/8.)/pi (see <tt class="xref py py-func docutils literal"><span class="pre">BFactor2RMSF()</span></tt>).</p>
+sigma is taken as sqrt(3.*B/8.)/pi (see <code class="xref py py-func docutils literal"><span class="pre">BFactor2RMSF()</span></code>).</p>
 <p>Construct the density from psf and pdb and the atomselection.</p>
 <blockquote>
 <div><dl class="docutils">
@@ -691,13 +688,13 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt>pdb</dt>
-<dd><p class="first last">PDB file or <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt>; a PDB is read with the
+<dd><p class="first last">PDB file or <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code>; a PDB is read with the
 simpl PDB reader. If the Bio.PDB reader is required, either set
-the <em>permissive_pdb_reader</em> flag to <tt class="docutils literal"><span class="pre">False</span></tt> in
-<tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> or supply a Universe
-that was created with the <cite>permissive</cite> = <tt class="docutils literal"><span class="pre">False</span></tt> keyword.</p>
+the <em>permissive_pdb_reader</em> flag to <code class="docutils literal"><span class="pre">False</span></code> in
+<code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> or supply a Universe
+that was created with the <cite>permissive</cite> = <code class="docutils literal"><span class="pre">False</span></code> keyword.</p>
 </dd>
 <dt>atomselection</dt>
 <dd><p class="first last">selection string (MDAnalysis syntax) for the species to be analyzed</p>
@@ -725,7 +722,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 that can be easily matched to a broader density distribution.</p>
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.BfactorDensityCreator.Density">
-<tt class="descname">Density</tt><big>(</big><em>threshold=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#BfactorDensityCreator.Density"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.BfactorDensityCreator.Density" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Density</code><span class="sig-paren">(</span><em>threshold=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/density.html#BfactorDensityCreator.Density"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.density.BfactorDensityCreator.Density" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a Density object.</p>
 </dd></dl>
 
@@ -733,7 +730,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.density.Grid">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.density.</tt><tt class="descname">Grid</tt><big>(</big><em>grid=None</em>, <em>edges=None</em>, <em>origin=None</em>, <em>delta=None</em>, <em>metadata=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Grid" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.density.</code><code class="descname">Grid</code><span class="sig-paren">(</span><em>grid=None</em>, <em>edges=None</em>, <em>origin=None</em>, <em>delta=None</em>, <em>metadata=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Grid" title="Permalink to this definition">¶</a></dt>
 <dd><p>Class to manage a multidimensional grid object.</p>
 <p>The export(format=&#8217;dx&#8217;) method always exports a 3D object, the
 rest should work for an array of any dimension.</p>
@@ -758,8 +755,8 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
-<dt>grid</dt>
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
+<dt>grid       </dt>
 <dd><p class="first last">histogram or density, defined on numpy nD array</p>
 </dd>
 <dt>edges</dt>
@@ -770,7 +767,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <dd><p class="first last">cartesian coordinates of the center of grid[0,0,...,0]</p>
 </dd>
 <dt>delta</dt>
-<dd><p class="first last">Either n x n array containing the cell lengths in each dimension,
+<dd><p class="first last">Either n x n array containing the cell lengths in each dimension, 
 or n x 1 array for rectangular arrays.</p>
 </dd>
 <dt>metadata</dt>
@@ -788,13 +785,13 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 </table>
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Grid.centers">
-<tt class="descname">centers</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.centers" title="Permalink to this definition">¶</a></dt>
+<code class="descname">centers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.centers" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns the coordinates of the centers of all grid cells as an iterator.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Grid.check_compatible">
-<tt class="descname">check_compatible</tt><big>(</big><em>other</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.check_compatible" title="Permalink to this definition">¶</a></dt>
+<code class="descname">check_compatible</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.check_compatible" title="Permalink to this definition">¶</a></dt>
 <dd><p>Check if <em>other</em> can be used in an arithmetic operation.</p>
 <ol class="arabic simple">
 <li><em>other</em> is a scalar</li>
@@ -804,7 +801,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><tt class="xref py py-exc docutils literal"><span class="pre">TypeError</span></tt> if not compatible.</td>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">TypeError</span></code> if not compatible.</td>
 </tr>
 </tbody>
 </table>
@@ -812,38 +809,35 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Grid.export">
-<tt class="descname">export</tt><big>(</big><em>filename</em>, <em>format=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.export" title="Permalink to this definition">¶</a></dt>
-<dd><p>export density to file using the given format.</p>
+<code class="descname">export</code><span class="sig-paren">(</span><em>filename</em>, <em>format=None</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.export" title="Permalink to this definition">¶</a></dt>
+<dd><p>export density to file using the given format; use &#8216;dx&#8217; for visualization.</p>
+<p>export(filename=&lt;filename&gt;,format=&lt;format&gt;)</p>
 <p>The format can also be deduced from the suffix of the filename
 though the <em>format</em> keyword takes precedence.</p>
-<p>The default format for export() is &#8216;dx&#8217;.  Use &#8216;dx&#8217; for
-visualization.</p>
-<p>Implemented formats:</p>
-<dl class="docutils">
-<dt>dx</dt>
-<dd><tt class="xref py py-mod docutils literal"><span class="pre">OpenDX</span></tt></dd>
-<dt>pickle</dt>
-<dd>pickle (use :meth:<tt class="docutils literal"><span class="pre">Grid.load`</span> <span class="pre">to</span> <span class="pre">restore);</span> <span class="pre">:meth:`Grid.save`</span>
-<span class="pre">is</span> <span class="pre">simpler</span> <span class="pre">than</span> <span class="pre">``export(format='python')</span></tt>.</dd>
-</dl>
+<p>The default format for export() is &#8216;dx&#8217;.</p>
+<p>Only implemented formats:</p>
+<p>dx        OpenDX
+pickle    pickle (use Grid.load(filename) to restore); Grid.save()</p>
+<blockquote>
+<div>is simpler than export(format=&#8217;python&#8217;).</div></blockquote>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.density.Grid.interpolated">
-<tt class="descname">interpolated</tt><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.interpolated" title="Permalink to this definition">¶</a></dt>
+<code class="descname">interpolated</code><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.interpolated" title="Permalink to this definition">¶</a></dt>
 <dd><p>B-spline function over the data grid(x,y,z).</p>
 <blockquote>
 <div>interpolated([x1,x2,...],[y1,y2,...],[z1,z2,...]) -&gt; F[x1,y1,z1],F[x2,y2,z2],...</div></blockquote>
-<p>The interpolation order is set in <tt class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_spline_order</span></tt>.</p>
+<p>The interpolation order is set in <code class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_spline_order</span></code>.</p>
 <p>The interpolated function is computed once and is cached for better
-performance. Whenever <tt class="xref py py-attr docutils literal"><span class="pre">interpolation_spline_order</span></tt> is
-modified, <a class="reference internal" href="#MDAnalysis.analysis.density.Grid.interpolated" title="MDAnalysis.analysis.density.Grid.interpolated"><tt class="xref py py-meth docutils literal"><span class="pre">Grid.interpolated()</span></tt></a> is recomputed.</p>
-<p>The value for unknown data is set in <tt class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_cval</span></tt>
+performance. Whenever <code class="xref py py-attr docutils literal"><span class="pre">interpolation_spline_order</span></code> is
+modified, <a class="reference internal" href="#MDAnalysis.analysis.density.Grid.interpolated" title="MDAnalysis.analysis.density.Grid.interpolated"><code class="xref py py-meth docutils literal"><span class="pre">Grid.interpolated()</span></code></a> is recomputed.</p>
+<p>The value for unknown data is set in <code class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_cval</span></code>
 (TODO: also recompute when interpolation_cval value is changed.)</p>
 <dl class="docutils">
 <dt>Example usage for resampling::</dt>
 <dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">XX</span><span class="p">,</span><span class="n">YY</span><span class="p">,</span><span class="n">ZZ</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">mgrid</span><span class="p">[</span><span class="mi">40</span><span class="p">:</span><span class="mi">75</span><span class="p">:</span><span class="mf">0.5</span><span class="p">,</span> <span class="mi">96</span><span class="p">:</span><span class="mi">150</span><span class="p">:</span><span class="mf">0.5</span><span class="p">,</span> <span class="mi">20</span><span class="p">:</span><span class="mi">50</span><span class="p">:</span><span class="mf">0.5</span><span class="p">]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">FF</span> <span class="o">=</span> <span class="n">interpolated</span><span class="p">(</span><span class="n">XX</span><span class="p">,</span><span class="n">YY</span><span class="p">,</span><span class="n">ZZ</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">FF</span> <span class="o">=</span> <span class="n">interpolated</span><span class="p">(</span><span class="n">XX</span><span class="p">,</span><span class="n">YY</span><span class="p">,</span><span class="n">ZZ</span><span class="p">)</span>            
 </pre></div>
 </div>
 </dd>
@@ -852,7 +846,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Grid.load">
-<tt class="descname">load</tt><big>(</big><em>filename</em>, <em>format=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.load" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load</code><span class="sig-paren">(</span><em>filename</em>, <em>format=None</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.load" title="Permalink to this definition">¶</a></dt>
 <dd><p>Load saved (pickled or dx) grid and edges from &lt;filename&gt;.pickle</p>
 <blockquote>
 <div>Grid.load(&lt;filename&gt;.pickle)
@@ -863,7 +857,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Grid.resample">
-<tt class="descname">resample</tt><big>(</big><em>edges</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.resample" title="Permalink to this definition">¶</a></dt>
+<code class="descname">resample</code><span class="sig-paren">(</span><em>edges</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.resample" title="Permalink to this definition">¶</a></dt>
 <dd><p>Resample data to a new grid with edges <em>edges</em>.</p>
 <blockquote>
 <div>resample(edges) &#8211;&gt; Grid</div></blockquote>
@@ -871,18 +865,18 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
 <blockquote>
 <div>resample(otherGrid) &#8211;&gt; Grid</div></blockquote>
 <p>The order of the interpolation is set by
-<tt class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_spline_order</span></tt>.</p>
+<code class="xref py py-attr docutils literal"><span class="pre">Grid.interpolation_spline_order</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Grid.resample_factor">
-<tt class="descname">resample_factor</tt><big>(</big><em>factor</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.resample_factor" title="Permalink to this definition">¶</a></dt>
+<code class="descname">resample_factor</code><span class="sig-paren">(</span><em>factor</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.resample_factor" title="Permalink to this definition">¶</a></dt>
 <dd><p>Resample to a new regular grid with factor*oldN cells along each dimension.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.density.Grid.save">
-<tt class="descname">save</tt><big>(</big><em>filename</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.density.Grid.save" title="Permalink to this definition">¶</a></dt>
 <dd><p>Save a grid object to &lt;filename&gt;.pickle</p>
 <blockquote>
 <div>Grid.save(filename)</div></blockquote>
@@ -903,7 +897,7 @@ <h2>3.6.1.2. Classes and Functions<a class="headerlink" href="#classes-and-funct
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
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         <li class="right" style="margin-right: 10px">
@@ -918,11 +912,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="helanal.html" title="3.5.2. HELANAL — analysis of protein helices"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -932,7 +926,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/distances.html b/package/doc/html/documentation_pages/analysis/distances.html
index 48560343b42..af5b42b6eeb 100644
--- a/package/doc/html/documentation_pages/analysis/distances.html
+++ b/package/doc/html/documentation_pages/analysis/distances.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.1.3. Distance analysis — MDAnalysis.analysis.distances &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.1.3. Distance analysis — MDAnalysis.analysis.distances &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
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@@ -16,7 +14,7 @@
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+        VERSION:     '0.11.0',
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         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
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-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="3.1.4. Calculating root mean square quantities — MDAnalysis.analysis.rms" href="rms.html" />
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+    <div class="related" role="navigation" aria-label="related navigation">
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              accesskey="P">previous</a> |</li>
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+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
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+                        title="previous chapter">3.1.2. Native contacts analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></code></a></p>
   <h4>Next topic</h4>
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-  <h3>This Page</h3>
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+                        title="next chapter">3.1.4. Calculating root mean square quantities &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
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+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.distances"></span><div class="section" id="distance-analysis-mdanalysis-analysis-distances">
-<h1>3.1.3. Distance analysis &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.distances" title="MDAnalysis.analysis.distances"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.distances</span></tt></a><a class="headerlink" href="#distance-analysis-mdanalysis-analysis-distances" title="Permalink to this headline">¶</a></h1>
+<h1>3.1.3. Distance analysis &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.distances" title="MDAnalysis.analysis.distances"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.distances</span></code></a><a class="headerlink" href="#distance-analysis-mdanalysis-analysis-distances" title="Permalink to this headline">¶</a></h1>
 <p>This module provides functions to rapidly compute distances between
 atoms or groups of atoms.</p>
-<p><a class="reference internal" href="#MDAnalysis.analysis.distances.dist" title="MDAnalysis.analysis.distances.dist"><tt class="xref py py-func docutils literal"><span class="pre">dist()</span></tt></a> and <tt class="xref py py-func docutils literal"><span class="pre">between()</span></tt> can take atom groups that do not even
-have to be from the same <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>.</p>
-<div class="admonition-see-also admonition seealso">
+<p><a class="reference internal" href="#MDAnalysis.analysis.distances.dist" title="MDAnalysis.analysis.distances.dist"><code class="xref py py-func docutils literal"><span class="pre">dist()</span></code></a> and <code class="xref py py-func docutils literal"><span class="pre">between()</span></code> can take atom groups that do not even
+have to be from the same <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>.</p>
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../lib/distances.html#module-MDAnalysis.lib.distances" title="MDAnalysis.lib.distances"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.distances</span></tt></a> and <a class="reference internal" href="../lib/parallel.html#module-MDAnalysis.lib.parallel.distances" title="MDAnalysis.lib.parallel.distances"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.parallel.distances</span></tt></a></p>
+<p class="last"><a class="reference internal" href="../lib/distances.html#module-MDAnalysis.lib.distances" title="MDAnalysis.lib.distances"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.distances</span></code></a> and <a class="reference internal" href="../lib/parallel.html#module-MDAnalysis.lib.parallel.distances" title="MDAnalysis.lib.parallel.distances"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.parallel.distances</span></code></a></p>
 </div>
 <dl class="function">
 <dt id="MDAnalysis.analysis.distances.distance_array">
-<tt class="descclassname">MDAnalysis.analysis.distances.</tt><tt class="descname">distance_array</tt><big>(</big><em>reference</em>, <em>configuration</em>, <em>box=None</em>, <em>result=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.distances.distance_array" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.distances.</code><code class="descname">distance_array</code><span class="sig-paren">(</span><em>reference</em>, <em>configuration</em>, <em>box=None</em>, <em>result=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#distance_array"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.distances.distance_array" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate all distances between a reference set and another configuration.</p>
 <p>If there are <em>i</em> positions in reference, and <em>j</em> positions in configuration,
 will calculate a <em>i</em> x <em>j</em> array of distances
 If an <em>box</em> is supplied then a minimum image convention is used when
 calculating distances.</p>
-<p>If a 2D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with the shape <tt class="docutils literal"><span class="pre">(len(reference),</span>
-<span class="pre">len(configuration))</span></tt> is provided in <em>result</em> then this preallocated array is
+<p>If a 2D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with the shape <code class="docutils literal"><span class="pre">(len(reference),</span>
+<span class="pre">len(configuration))</span></code> is provided in <em>result</em> then this preallocated array is
 filled. This can speed up calculations.</p>
 <p>d = distance_array(reference, configuration[,box[,result=d]])</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>reference</em></dt>
 <dd><p class="first last">reference coordinate array (must be numpy.float32)</p>
 </dd>
@@ -127,21 +127,21 @@ <h1>3.1.3. Distance analysis &#8212; <a class="reference internal" href="#module
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">cell dimensions (minimum image convention is applied)
-or None [<tt class="docutils literal"><span class="pre">None</span></tt>].
+or None [<code class="docutils literal"><span class="pre">None</span></code>].
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
 <dd><p class="first last">optional preallocated result array which must have the
 shape (len(ref), len(conf)) and dtype=numpy.float64.
 Avoids creating the array which saves time when the function
-is called repeatedly. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+is called repeatedly. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>d</em></dt>
 <dd><p class="first last">(len(reference),len(configuration)) numpy array with the distances d[i,j]
 between reference coordinates i and configuration coordinates j</p>
@@ -160,38 +160,38 @@ <h1>3.1.3. Distance analysis &#8212; <a class="reference internal" href="#module
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.distances.self_distance_array">
-<tt class="descclassname">MDAnalysis.analysis.distances.</tt><tt class="descname">self_distance_array</tt><big>(</big><em>reference</em>, <em>box=None</em>, <em>result=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.distances.self_distance_array" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.distances.</code><code class="descname">self_distance_array</code><span class="sig-paren">(</span><em>reference</em>, <em>box=None</em>, <em>result=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#self_distance_array"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.distances.self_distance_array" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate all distances within a configuration <em>reference</em>.</p>
 <p>If a <em>box</em> is supplied then a minimum image convention is used before
 calculating distances.</p>
-<p>If a 1D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with the shape
-<tt class="docutils literal"><span class="pre">(N*(N-1)/2)</span></tt> is provided in <em>result</em> then this preallocated array
+<p>If a 1D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with the shape
+<code class="docutils literal"><span class="pre">(N*(N-1)/2)</span></code> is provided in <em>result</em> then this preallocated array
 is filled. This can speed up calculations.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>ref</em></dt>
 <dd><p class="first last">reference coordinate array with N=len(ref) coordinates</p>
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">cell dimensions (minimum image convention is applied)
-or None [<tt class="docutils literal"><span class="pre">None</span></tt>]
+or None [<code class="docutils literal"><span class="pre">None</span></code>]
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
 <dd><p class="first last">optional preallocated result array which must have the shape
-(N*(N-1)/2,) and dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt>. Avoids creating
+(N*(N-1)/2,) and dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code>. Avoids creating
 the array which saves time when the function is called
-repeatedly. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+repeatedly. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>d</em></dt>
 <dd><p class="first">N*(N-1)/2 numpy 1D array with the distances dist[i,j] between ref
 coordinates i and j at position d[k]. Loop through d:</p>
@@ -216,21 +216,22 @@ <h1>3.1.3. Distance analysis &#8212; <a class="reference internal" href="#module
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.distances.contact_matrix">
-<tt class="descclassname">MDAnalysis.analysis.distances.</tt><tt class="descname">contact_matrix</tt><big>(</big><em>coord</em>, <em>cutoff=15.0</em>, <em>returntype='numpy'</em>, <em>box=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/distances.html#contact_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.distances.contact_matrix" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.distances.</code><code class="descname">contact_matrix</code><span class="sig-paren">(</span><em>coord</em>, <em>cutoff=15.0</em>, <em>returntype='numpy'</em>, <em>box=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/distances.html#contact_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.distances.contact_matrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculates a matrix of contacts within a numpy array of type float32.</p>
 <p>There is a fast, high-memory-usage version for small systems
 (<em>returntype</em> = &#8216;numpy&#8217;), and a slower, low-memory-usage version for
 larger systems (<em>returntype</em> = &#8216;sparse&#8217;).</p>
-<p>If <em>box</em> dimensions are passed (<tt class="docutils literal"><span class="pre">box</span> <span class="pre">=</span> <span class="pre">[Lx,</span> <span class="pre">Ly,</span> <span class="pre">Lz]</span></tt>), then
+<p>If <em>box</em> dimensions are passed (<code class="docutils literal"><span class="pre">box</span> <span class="pre">=</span> <span class="pre">[Lx,</span> <span class="pre">Ly,</span> <span class="pre">Lz]</span></code>), then
 periodic boundary conditions are applied.  Only orthorhombic boxes
 are currently supported.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Keyword <em>suppress_progmet</em> and <em>progress_meter_freq</em> were removed.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Keyword <em>suppress_progmet</em> and <em>progress_meter_freq</em> were removed.</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.distances.dist">
-<tt class="descclassname">MDAnalysis.analysis.distances.</tt><tt class="descname">dist</tt><big>(</big><em>A</em>, <em>B</em>, <em>offset=0</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/distances.html#dist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.distances.dist" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.distances.</code><code class="descname">dist</code><span class="sig-paren">(</span><em>A</em>, <em>B</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/distances.html#dist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.distances.dist" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return distance between atoms in two atom groups.</p>
 <p>The distance is calculated atom-wise. The residue ids are also
 returned because a typical use case is to look at CA distances
@@ -241,15 +242,15 @@ <h1>3.1.3. Distance analysis &#8212; <a class="reference internal" href="#module
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>A</em>, <em>B</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> with the
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> with the
 same number of atoms</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>offset</em> <span class="classifier-delimiter">:</span> <span class="classifier">integer</span></dt>
 <dd><p class="first last">The <em>offset</em> is added to <em>resids_A</em> and <em>resids_B</em> (see
 below) in order to produce PDB numbers. The default is 0.</p>
@@ -263,7 +264,7 @@ <h1>3.1.3. Distance analysis &#8212; <a class="reference internal" href="#module
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">NumPy <cite>array([resids_A, resids_B, distances])</cite></p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">NumPy <cite>array([resids_A, resids_B, distances])</cite></p>
 </td>
 </tr>
 </tbody>
@@ -278,7 +279,7 @@ <h1>3.1.3. Distance analysis &#8212; <a class="reference internal" href="#module
       </div>
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-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
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@@ -293,11 +294,11 @@ <h3>Navigation</h3>
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-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
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     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
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@@ -307,7 +308,7 @@ <h3>Navigation</h3>
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/gnm.html b/package/doc/html/documentation_pages/analysis/gnm.html
index 49ecd017378..d9901af1486 100644
--- a/package/doc/html/documentation_pages/analysis/gnm.html
+++ b/package/doc/html/documentation_pages/analysis/gnm.html
@@ -1,5 +1,3 @@
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 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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@@ -8,7 +6,7 @@
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+    <title>3.5.1. Elastic network analysis of MD trajectories — MDAnalysis.analysis.gnm &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
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     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
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+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
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+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
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   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.5.1. Elastic network analysis of MD trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.gnm</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.5.1. Elastic network analysis of MD trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.gnm</span></code></a><ul>
 <li><a class="reference internal" href="#analysis-tasks">3.5.1.1. Analysis tasks</a></li>
 <li><a class="reference internal" href="#utility-functions">3.5.1.2. Utility functions</a></li>
 </ul>
@@ -71,16 +69,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
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-                        title="previous chapter">3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.x3dna</span></tt></a></p>
+                        title="previous chapter">3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.x3dna</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="helanal.html"
                         title="next chapter">3.5.2. HELANAL &#8212; analysis of protein helices</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/analysis/gnm.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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+  <div role="note" aria-label="source link">
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@@ -99,10 +99,10 @@ <h3>Quick search</h3>
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   <span class="target" id="module-MDAnalysis.analysis.gnm"></span><div class="section" id="elastic-network-analysis-of-md-trajectories-mdanalysis-analysis-gnm">
-<h1>3.5.1. Elastic network analysis of MD trajectories &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.gnm" title="MDAnalysis.analysis.gnm"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.gnm</span></tt></a><a class="headerlink" href="#elastic-network-analysis-of-md-trajectories-mdanalysis-analysis-gnm" title="Permalink to this headline">¶</a></h1>
+<h1>3.5.1. Elastic network analysis of MD trajectories &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.gnm" title="MDAnalysis.analysis.gnm"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.gnm</span></code></a><a class="headerlink" href="#elastic-network-analysis-of-md-trajectories-mdanalysis-analysis-gnm" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -115,9 +115,9 @@ <h1>3.5.1. Elastic network analysis of MD trajectories &#8212; <a class="referen
 </tr>
 </tbody>
 </table>
-<p>Analyse a trajectory using elastic network models, following the approach of <a class="reference internal" href="#hall2007">[Hall2007]</a>.</p>
-<p>An example is provided in <tt class="file docutils literal"><span class="pre">examples/GNMExample.py</span></tt>. The basic
-approach is to pass a trajectory to <a class="reference internal" href="#MDAnalysis.analysis.gnm.GNMAnalysis" title="MDAnalysis.analysis.gnm.GNMAnalysis"><tt class="xref py py-class docutils literal"><span class="pre">GNMAnalysis</span></tt></a> and then run
+<p>Analyse a trajectory using elastic network models, following the approach of <a class="reference internal" href="#hall2007" id="id1">[Hall2007]</a>.</p>
+<p>An example is provided in <code class="file docutils literal"><span class="pre">examples/GNMExample.py</span></code>. The basic
+approach is to pass a trajectory to <a class="reference internal" href="#MDAnalysis.analysis.gnm.GNMAnalysis" title="MDAnalysis.analysis.gnm.GNMAnalysis"><code class="xref py py-class docutils literal"><span class="pre">GNMAnalysis</span></code></a> and then run
 the analysis:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">u</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span><span class="p">)</span>
 <span class="n">C</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">analysis</span><span class="o">.</span><span class="n">gnm</span><span class="o">.</span><span class="n">GNMAnalysis</span><span class="p">(</span><span class="n">u</span><span class="p">,</span><span class="n">ReportVector</span><span class="o">=</span><span class="s">&quot;output.txt&quot;</span><span class="p">)</span>
@@ -131,8 +131,8 @@ <h1>3.5.1. Elastic network analysis of MD trajectories &#8212; <a class="referen
 <span class="n">outputfile</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
 </pre></div>
 </div>
-<p>The results are found in <tt class="xref py py-attr docutils literal"><span class="pre">GNMAnalysis.results</span></tt>, which can be
-used for further processing (see <a class="reference internal" href="#hall2007">[Hall2007]</a>).</p>
+<p>The results are found in <code class="xref py py-attr docutils literal"><span class="pre">GNMAnalysis.results</span></code>, which can be
+used for further processing (see <a class="reference internal" href="#hall2007" id="id2">[Hall2007]</a>).</p>
 <p class="rubric">References</p>
 <table class="docutils citation" frame="void" id="hall2007" rules="none">
 <colgroup><col class="label" /><col /></colgroup>
@@ -146,7 +146,7 @@ <h1>3.5.1. Elastic network analysis of MD trajectories &#8212; <a class="referen
 <h2>3.5.1.1. Analysis tasks<a class="headerlink" href="#analysis-tasks" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.analysis.gnm.GNMAnalysis">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.gnm.</tt><tt class="descname">GNMAnalysis</tt><big>(</big><em>universe</em>, <em>selection='protein and name CA'</em>, <em>cutoff=7.0</em>, <em>ReportVector=None</em>, <em>Bonus_groups=()</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#GNMAnalysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.GNMAnalysis" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.gnm.</code><code class="descname">GNMAnalysis</code><span class="sig-paren">(</span><em>universe</em>, <em>selection='protein and name CA'</em>, <em>cutoff=7.0</em>, <em>ReportVector=None</em>, <em>Bonus_groups=()</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#GNMAnalysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.GNMAnalysis" title="Permalink to this definition">¶</a></dt>
 <dd><p>Basic tool for GNM analysis.</p>
 <p>Each frame is treated as a novel structure and the GNM
 calculated.  By default, this stores the dominant eigenvector
@@ -154,7 +154,7 @@ <h2>3.5.1.1. Analysis tasks<a class="headerlink" href="#analysis-tasks" title="P
 conformational change in a simulation.</p>
 <dl class="method">
 <dt id="MDAnalysis.analysis.gnm.GNMAnalysis.generate_kirchoff">
-<tt class="descname">generate_kirchoff</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#GNMAnalysis.generate_kirchoff"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.GNMAnalysis.generate_kirchoff" title="Permalink to this definition">¶</a></dt>
+<code class="descname">generate_kirchoff</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#GNMAnalysis.generate_kirchoff"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.GNMAnalysis.generate_kirchoff" title="Permalink to this definition">¶</a></dt>
 <dd><p>Generate the Kirchhoff matrix of contacts.</p>
 <p>This generates the neighbour matrix by generating a grid of
 near-neighbours and then calculating which are are within
@@ -163,7 +163,7 @@ <h2>3.5.1.1. Analysis tasks<a class="headerlink" href="#analysis-tasks" title="P
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.gnm.GNMAnalysis.generate_output">
-<tt class="descname">generate_output</tt><big>(</big><em>w</em>, <em>v</em>, <em>outputobject</em>, <em>time</em>, <em>matrix</em>, <em>nmodes=2</em>, <em>ReportVector=None</em>, <em>counter=0</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#GNMAnalysis.generate_output"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.GNMAnalysis.generate_output" title="Permalink to this definition">¶</a></dt>
+<code class="descname">generate_output</code><span class="sig-paren">(</span><em>w</em>, <em>v</em>, <em>outputobject</em>, <em>time</em>, <em>matrix</em>, <em>nmodes=2</em>, <em>ReportVector=None</em>, <em>counter=0</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#GNMAnalysis.generate_output"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.GNMAnalysis.generate_output" title="Permalink to this definition">¶</a></dt>
 <dd><p>Appends eigenvalues and eigenvectors to results.</p>
 <p>This generates the output by adding eigenvalue and
 eigenvector data to an appendable object and optionally
@@ -174,10 +174,11 @@ <h2>3.5.1.1. Analysis tasks<a class="headerlink" href="#analysis-tasks" title="P
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.gnm.GNMAnalysis.run">
-<tt class="descname">run</tt><big>(</big><em>skip=1</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#GNMAnalysis.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.GNMAnalysis.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>skip=1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#GNMAnalysis.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.GNMAnalysis.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Analyze trajectory and produce timeseries.</p>
 <p>Returns GNM results per frame:</p>
-<div class="highlight-python"><pre>results = [(time,eigenvalues[1],eigenvectors[1]),(time,eigenvalues[1],eigenvectors[1])... ]</pre>
+<div class="highlight-python"><div class="highlight"><pre>results = [(time,eigenvalues[1],eigenvectors[1]),(time,eigenvalues[1],eigenvectors[1])... ]
+</pre></div>
 </div>
 </dd></dl>
 
@@ -185,7 +186,7 @@ <h2>3.5.1.1. Analysis tasks<a class="headerlink" href="#analysis-tasks" title="P
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.gnm.closeContactGNMAnalysis">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.gnm.</tt><tt class="descname">closeContactGNMAnalysis</tt><big>(</big><em>universe</em>, <em>selection='protein'</em>, <em>cutoff=4.5</em>, <em>ReportVector=None</em>, <em>MassWeight=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#closeContactGNMAnalysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.closeContactGNMAnalysis" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.gnm.</code><code class="descname">closeContactGNMAnalysis</code><span class="sig-paren">(</span><em>universe</em>, <em>selection='protein'</em>, <em>cutoff=4.5</em>, <em>ReportVector=None</em>, <em>MassWeight=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#closeContactGNMAnalysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.closeContactGNMAnalysis" title="Permalink to this definition">¶</a></dt>
 <dd><p>GNMAnalysis only using close contacts.</p>
 <p>This is a version of the GNM where the Kirchoff matrix is
 constructed from the close contacts between individual atoms
@@ -199,13 +200,13 @@ <h2>3.5.1.2. Utility functions<a class="headerlink" href="#utility-functions" ti
 directly needed to perform the analysis.</p>
 <dl class="function">
 <dt id="MDAnalysis.analysis.gnm.backup_file">
-<tt class="descclassname">MDAnalysis.analysis.gnm.</tt><tt class="descname">backup_file</tt><big>(</big><em>filename</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#backup_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.backup_file" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.gnm.</code><code class="descname">backup_file</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#backup_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.backup_file" title="Permalink to this definition">¶</a></dt>
 <dd><p>This function helps prevent overwriting default named files</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.gnm.generate_grid">
-<tt class="descclassname">MDAnalysis.analysis.gnm.</tt><tt class="descname">generate_grid</tt><big>(</big><em>positions</em>, <em>cutoff</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#generate_grid"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.generate_grid" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.gnm.</code><code class="descname">generate_grid</code><span class="sig-paren">(</span><em>positions</em>, <em>cutoff</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#generate_grid"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.generate_grid" title="Permalink to this definition">¶</a></dt>
 <dd><p>An alternative to searching the entire list of each atom; divide the structure into cutoff sized boxes
 This way, for each particle you only need to search the neighbouring boxes to find the particles within the cutoff
 Observed a 6x speed up for a smallish protein with ~300 residues; this should get better with bigger systems.</p>
@@ -213,7 +214,7 @@ <h2>3.5.1.2. Utility functions<a class="headerlink" href="#utility-functions" ti
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.gnm.order_list">
-<tt class="descclassname">MDAnalysis.analysis.gnm.</tt><tt class="descname">order_list</tt><big>(</big><em>w</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#order_list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.order_list" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.gnm.</code><code class="descname">order_list</code><span class="sig-paren">(</span><em>w</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/gnm.html#order_list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.gnm.order_list" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a dictionary showing the order of eigenvalues (which are reported scrambled normally)</p>
 </dd></dl>
 
@@ -226,7 +227,7 @@ <h2>3.5.1.2. Utility functions<a class="headerlink" href="#utility-functions" ti
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -241,11 +242,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="x3dna.html" title="3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles — MDAnalysis.analysis.x3dna"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -255,7 +256,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/hbond_analysis.html b/package/doc/html/documentation_pages/analysis/hbond_analysis.html
index 6514cfb1d99..fcfc97cb0e5 100644
--- a/package/doc/html/documentation_pages/analysis/hbond_analysis.html
+++ b/package/doc/html/documentation_pages/analysis/hbond_analysis.html
@@ -1,5 +1,3 @@
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-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
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   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.2.1. Hydrogen Bond analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_analysis</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.2.1. Hydrogen Bond analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_analysis</span></code></a><ul>
 <li><a class="reference internal" href="#output">3.2.1.1. Output</a></li>
 <li><a class="reference internal" href="#detection-of-hydrogen-bonds">3.2.1.2. Detection of hydrogen bonds</a></li>
 <li><a class="reference internal" href="#example">3.2.1.3. Example</a></li>
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   <span class="target" id="module-MDAnalysis.analysis.hbonds.hbond_analysis"></span><div class="section" id="hydrogen-bond-analysis-mdanalysis-analysis-hbonds-hbond-analysis">
-<h1>3.2.1. Hydrogen Bond analysis &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.hbonds.hbond_analysis" title="MDAnalysis.analysis.hbonds.hbond_analysis"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_analysis</span></tt></a><a class="headerlink" href="#hydrogen-bond-analysis-mdanalysis-analysis-hbonds-hbond-analysis" title="Permalink to this headline">¶</a></h1>
+<h1>3.2.1. Hydrogen Bond analysis &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.hbonds.hbond_analysis" title="MDAnalysis.analysis.hbonds.hbond_analysis"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_analysis</span></code></a><a class="headerlink" href="#hydrogen-bond-analysis-mdanalysis-analysis-hbonds-hbond-analysis" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -117,15 +117,15 @@ <h1>3.2.1. Hydrogen Bond analysis &#8212; <a class="reference internal" href="#m
 </tr>
 </tbody>
 </table>
-<p>Given a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> (simulation
+<p>Given a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> (simulation
 trajectory with 1 or more frames) measure all hydrogen bonds for each
 frame between selections 1 and 2.</p>
-<p>The <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis"><tt class="xref py py-class docutils literal"><span class="pre">HydrogenBondAnalysis</span></tt></a> class is modeled after the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/">VMD
+<p>The <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis"><code class="xref py py-class docutils literal"><span class="pre">HydrogenBondAnalysis</span></code></a> class is modeled after the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/">VMD
 HBONDS plugin</a>.</p>
 <dl class="docutils">
 <dt>Options:</dt>
 <dd><ul class="first last simple">
-<li><em>update_selections</em> (<tt class="docutils literal"><span class="pre">True</span></tt>): update selections at each frame?</li>
+<li><em>update_selections</em> (<code class="docutils literal"><span class="pre">True</span></code>): update selections at each frame?</li>
 <li><em>selection_1_type</em> (&#8220;both&#8221;): selection 1 is the: &#8220;donor&#8221;, &#8220;acceptor&#8221;, &#8220;both&#8221;</li>
 <li>donor-acceptor <em>distance</em> (Å): 3.0</li>
 <li>Angle <em>cutoff</em> (degrees): 120.0</li>
@@ -147,9 +147,9 @@ <h1>3.2.1. Hydrogen Bond analysis &#8212; <a class="reference internal" href="#m
 </dd>
 </dl>
 <p>Hydrogen bond data are returned per frame, which is stored in
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><tt class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></tt></a> (In the following description, <tt class="docutils literal"><span class="pre">#</span></tt>
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></code></a> (In the following description, <code class="docutils literal"><span class="pre">#</span></code>
 indicates comments that are not part of the output.):</p>
-<div class="highlight-python"><pre>results = [
+<div class="highlight-python"><div class="highlight"><pre>results = [
     [ # frame 1
        [ # hbond 1
           &lt;donor index&gt;, &lt;acceptor index&gt;, &lt;donor string&gt;, &lt;acceptor string&gt;, &lt;distance&gt;, &lt;angle&gt;
@@ -163,20 +163,21 @@ <h1>3.2.1. Hydrogen Bond analysis &#8212; <a class="reference internal" href="#m
       [ ... ], [ ... ], ...
     ],
     ...
-]</pre>
+]
+</pre></div>
 </div>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">For historic reasons, the <em>donor index</em> and <em>acceptor index</em> are a 1-based
-indices. To get the <tt class="xref py py-attr docutils literal"><span class="pre">Atom.index</span></tt> (the 0-based index typically used in
+indices. To get the <code class="xref py py-attr docutils literal"><span class="pre">Atom.index</span></code> (the 0-based index typically used in
 MDAnalysis simply subtract 1. For instance, to find an atom in
-<tt class="xref py py-attr docutils literal"><span class="pre">Universe.atoms</span></tt> by <em>index</em> from the output one would use
-<tt class="docutils literal"><span class="pre">u.atoms[index-1]</span></tt>.</p>
+<code class="xref py py-attr docutils literal"><span class="pre">Universe.atoms</span></code> by <em>index</em> from the output one would use
+<code class="docutils literal"><span class="pre">u.atoms[index-1]</span></code>.</p>
 </div>
-<p>Using the <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table"><tt class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis.generate_table()</span></tt></a> method one can reformat
+<p>Using the <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table"><code class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis.generate_table()</span></code></a> method one can reformat
 the results as a flat &#8220;normalised&#8221; table that is easier to import into a
-database for further processing. <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.save_table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.save_table"><tt class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis.save_table()</span></tt></a> saves
-the table to a pickled file. The table itself is a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></tt></a>.</p>
+database for further processing. <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.save_table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.save_table"><code class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis.save_table()</span></code></a> saves
+the table to a pickled file. The table itself is a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></code></a>.</p>
 </div>
 <div class="section" id="detection-of-hydrogen-bonds">
 <h2>3.2.1.2. Detection of hydrogen bonds<a class="headerlink" href="#detection-of-hydrogen-bonds" title="Permalink to this headline">¶</a></h2>
@@ -188,7 +189,7 @@ <h2>3.2.1.2. Detection of hydrogen bonds<a class="headerlink" href="#detection-o
 <em>angle</em> (default is 120º).</li>
 </ol>
 <p>The cut-off values <em>angle</em> and <em>distance</em> can be set as keywords to
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis"><tt class="xref py py-class docutils literal"><span class="pre">HydrogenBondAnalysis</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis"><code class="xref py py-class docutils literal"><span class="pre">HydrogenBondAnalysis</span></code></a>.</p>
 <p>Donor and acceptor heavy atoms are detected from atom names. The current
 defaults are appropriate for the CHARMM27 and GLYCAM06 force fields as defined
 in Table <a class="reference internal" href="#default-atom-names-for-hydrogen-bonding-analysis">Default atom names for hydrogen bonding analysis</a>.</p>
@@ -204,12 +205,13 @@ <h2>3.2.1.2. Detection of hydrogen bonds<a class="headerlink" href="#detection-o
 selects any atom whose name matches (name &#8220;H*&#8221; or name &#8220;[123]H&#8221;). For</div></blockquote>
 <p>The <em>distance</em> search is more rigorous but slower and is set as the
 default. Until release 0.7.6, only the heuristic search was implemented.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>Distance search added (see
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist"><tt class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis._get_bonded_hydrogens_dist()</span></tt></a>) and heuristic
-search improved (<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list"><tt class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis._get_bonded_hydrogens_list()</span></tt></a>)</p>
-<table border="1" class="docutils" id="default-atom-names-for-hydrogen-bonding-analysis">
-<caption>Default heavy atom names for CHARMM27 force field.</caption>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>Distance search added (see
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist"><code class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis._get_bonded_hydrogens_dist()</span></code></a>) and heuristic
+search improved (<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list"><code class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis._get_bonded_hydrogens_list()</span></code></a>)</p>
+</div>
+<table border="1" class="docutils" id="id2">
+<span id="default-atom-names-for-hydrogen-bonding-analysis"></span><caption><span class="caption-text">Default heavy atom names for CHARMM27 force field.</span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
 <colgroup>
 <col width="15%" />
 <col width="19%" />
@@ -297,7 +299,7 @@ <h2>3.2.1.2. Detection of hydrogen bonds<a class="headerlink" href="#detection-o
 <tr class="row-even"><td>MET</td>
 <td>&nbsp;</td>
 <td>SD</td>
-<td>see e.g. <a class="reference internal" href="#gregoret1991">[Gregoret1991]</a></td>
+<td>see e.g. <a class="reference internal" href="#gregoret1991" id="id1">[Gregoret1991]</a></td>
 </tr>
 <tr class="row-odd"><td>SER</td>
 <td>OG</td>
@@ -321,8 +323,8 @@ <h2>3.2.1.2. Detection of hydrogen bonds<a class="headerlink" href="#detection-o
 </tr>
 </tbody>
 </table>
-<table border="1" class="docutils">
-<caption>Heavy atom types for GLYCAM06 force field.</caption>
+<table border="1" class="docutils" id="id3">
+<caption><span class="caption-text">Heavy atom types for GLYCAM06 force field.</span><a class="headerlink" href="#id3" title="Permalink to this table">¶</a></caption>
 <colgroup>
 <col width="28%" />
 <col width="28%" />
@@ -358,7 +360,7 @@ <h2>3.2.1.2. Detection of hydrogen bonds<a class="headerlink" href="#detection-o
 <cite>Carbohydrate Naming Convention in Glycam</cite>.</p>
 <p>The lists of donor and acceptor names can be extended by providing lists of
 atom names in the <em>donors</em> and <em>acceptors</em> keywords to
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis"><tt class="xref py py-class docutils literal"><span class="pre">HydrogenBondAnalysis</span></tt></a>. If the lists are entirely inappropriate
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis"><code class="xref py py-class docutils literal"><span class="pre">HydrogenBondAnalysis</span></code></a>. If the lists are entirely inappropriate
 (e.g. when analysing simulations done with a force field that uses very
 different atom names) then one should either use the value &#8220;other&#8221; for <em>forcefield</em>
 to set no default values, or derive a new class and set the default list oneself:</p>
@@ -391,11 +393,11 @@ <h2>3.2.1.3. Example<a class="headerlink" href="#example" title="Permalink to th
 </pre></div>
 </div>
 <p>The results are stored as the attribute
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><tt class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></tt></a>; see <a class="reference internal" href="#analysis-output"><em>Output</em></a>
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></code></a>; see <a class="reference internal" href="#analysis-output"><span>Output</span></a>
 for the format and further options.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">Due to the way <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis"><tt class="xref py py-class docutils literal"><span class="pre">HydrogenBondAnalysis</span></tt></a> is implemented, it is
+<p class="last">Due to the way <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis"><code class="xref py py-class docutils literal"><span class="pre">HydrogenBondAnalysis</span></code></a> is implemented, it is
 more efficient to have the second selection (<em>selection2</em>) be the
 <em>larger</em> group, e.g. the water when looking at water-protein
 H-bonds or the whole protein when looking at ligand-protein
@@ -406,12 +408,12 @@ <h2>3.2.1.3. Example<a class="headerlink" href="#example" title="Permalink to th
 <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.hbonds.hbond_analysis.</tt><tt class="descname">HydrogenBondAnalysis</tt><big>(</big><em>universe</em>, <em>selection1='protein'</em>, <em>selection2='all'</em>, <em>selection1_type='both'</em>, <em>update_selection1=True</em>, <em>update_selection2=True</em>, <em>filter_first=True</em>, <em>distance_type='hydrogen'</em>, <em>distance=3.0</em>, <em>angle=120.0</em>, <em>forcefield='CHARMM27'</em>, <em>donors=None</em>, <em>acceptors=None</em>, <em>start=None</em>, <em>stop=None</em>, <em>step=None</em>, <em>verbose=False</em>, <em>detect_hydrogens='distance'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.hbonds.hbond_analysis.</code><code class="descname">HydrogenBondAnalysis</code><span class="sig-paren">(</span><em>universe</em>, <em>selection1='protein'</em>, <em>selection2='all'</em>, <em>selection1_type='both'</em>, <em>update_selection1=True</em>, <em>update_selection2=True</em>, <em>filter_first=True</em>, <em>distance_type='hydrogen'</em>, <em>distance=3.0</em>, <em>angle=120.0</em>, <em>forcefield='CHARMM27'</em>, <em>donors=None</em>, <em>acceptors=None</em>, <em>start=None</em>, <em>stop=None</em>, <em>step=None</em>, <em>verbose=False</em>, <em>detect_hydrogens='distance'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="Permalink to this definition">¶</a></dt>
 <dd><p>Perform a hydrogen bond analysis</p>
 <p>The analysis of the trajectory is performed with the
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.run" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.run"><tt class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis.run()</span></tt></a> method. The result is stored in
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><tt class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></tt></a>. See
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.run" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.run"><tt class="xref py py-meth docutils literal"><span class="pre">run()</span></tt></a> for the format.</p>
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.run" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.run"><code class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis.run()</span></code></a> method. The result is stored in
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></code></a>. See
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.run" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.run"><code class="xref py py-meth docutils literal"><span class="pre">run()</span></code></a> for the format.</p>
 <p>The default atom names are taken from the CHARMM 27 force field files, which
 will also work for e.g. OPLS/AA in Gromacs, and GLYCAM06.</p>
 <dl class="docutils">
@@ -434,25 +436,26 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </dl>
 </dd>
 </dl>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last">Table <a class="reference internal" href="#default-atom-names-for-hydrogen-bonding-analysis"><em>Default heavy atom names for CHARMM27 force field.</em></a></p>
+<p class="last">Table <a class="reference internal" href="#default-atom-names-for-hydrogen-bonding-analysis"><span>Default heavy atom names for CHARMM27 force field.</span></a></p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>DEFAULT_DONORS/ACCEPTORS is now embedded in a dict to switch between
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>DEFAULT_DONORS/ACCEPTORS is now embedded in a dict to switch between
 default values for different force fields.</p>
+</div>
 <p>Set up calculation of hydrogen bonds between two selections in a universe.</p>
-<p>The timeseries is accessible as the attribute <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><tt class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></tt></a>.</p>
+<p>The timeseries is accessible as the attribute <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></code></a>.</p>
 <p>Some initial checks are performed. If there are no atoms selected by
 <em>selection1</em> or <em>selection2</em> or if no donor hydrogens or acceptor atoms
-are found then a <tt class="xref py py-exc docutils literal"><span class="pre">SelectionError</span></tt> is raised for any selection that
+are found then a <code class="xref py py-exc docutils literal"><span class="pre">SelectionError</span></code> is raised for any selection that
 does <em>not</em> update (<em>update_selection1</em> and <em>update_selection2</em>
 keywords). For selections that are set to update, only a warning is
 logged because it is assumed that the selection might contain atoms at
 a later frame (e.g. for distance based selections).</p>
 <p>If no hydrogen bonds are detected or if the initial check fails, look
-at the log output (enable with <a class="reference internal" href="../lib/log.html#MDAnalysis.start_logging" title="MDAnalysis.start_logging"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.start_logging()</span></tt></a> and set
-<em>verbose</em> = <tt class="docutils literal"><span class="pre">True</span></tt>). It is likely that the default names for donors
+at the log output (enable with <a class="reference internal" href="../lib/log.html#MDAnalysis.start_logging" title="MDAnalysis.start_logging"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.start_logging()</span></code></a> and set
+<em>verbose</em> = <code class="docutils literal"><span class="pre">True</span></code>). It is likely that the default names for donors
 and acceptors are not suitable (especially for non-standard
 ligands). In this case, either change the <em>forcefield</em> or use
 customized <em>donors</em> and/or <em>acceptors</em>.</p>
@@ -460,22 +463,22 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 <p class="first admonition-title">Note</p>
 <p>In order to speed up processing, atoms are filtered by a coarse
 distance criterion before a detailed hydrogen bonding analysis is
-performed (<em>filter_first</em> = <tt class="docutils literal"><span class="pre">True</span></tt>). If one of your selections is
+performed (<em>filter_first</em> = <code class="docutils literal"><span class="pre">True</span></code>). If one of your selections is
 e.g. the solvent then <em>update_selection1</em> (or <em>update_selection2</em>)
-must also be <tt class="docutils literal"><span class="pre">True</span></tt> so that the list of candidate atoms is updated
+must also be <code class="docutils literal"><span class="pre">True</span></code> so that the list of candidate atoms is updated
 at each step: this is now the default.</p>
 <p class="last">If your selections will essentially remain the same for all time
 steps (i.e. residues are not moving farther than 3 x <em>distance</em>), for
 instance, if no water or large conformational changes are involved
-or if the optimization is disabled (<em>filter_first</em> = <tt class="docutils literal"><span class="pre">False</span></tt>) then
+or if the optimization is disabled (<em>filter_first</em> = <code class="docutils literal"><span class="pre">False</span></code>) then
 you can improve performance by setting the <em>update_selection</em>
-keywords to <tt class="docutils literal"><span class="pre">False</span></tt>.</p>
+keywords to <code class="docutils literal"><span class="pre">False</span></code>.</p>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Universe object</p>
 </dd>
@@ -494,13 +497,13 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 [&#8216;both&#8217;].</p>
 </dd>
 <dt><em>update_selection1</em></dt>
-<dd><p class="first last">Update selection 1 at each frame? [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Update selection 1 at each frame? [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>update_selection2</em></dt>
-<dd><p class="first last">Update selection 2 at each frame? [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Update selection 2 at each frame? [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>filter_first</em></dt>
-<dd><p class="first last">Filter selection 2 first to only atoms 3*distance away [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">Filter selection 2 first to only atoms 3*distance away [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 <dt><em>distance</em></dt>
 <dd><p class="first last">Distance cutoff for hydrogen bonds; only interactions with a H-A distance
@@ -515,36 +518,36 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </dd>
 <dt><em>forcefield</em></dt>
 <dd><p class="first last">Name of the forcefield used. Switches between different
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_DONORS" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_DONORS"><tt class="xref py py-attr docutils literal"><span class="pre">DEFAULT_DONORS</span></tt></a> and
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_ACCEPTORS" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_ACCEPTORS"><tt class="xref py py-attr docutils literal"><span class="pre">DEFAULT_ACCEPTORS</span></tt></a> values.
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_DONORS" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_DONORS"><code class="xref py py-attr docutils literal"><span class="pre">DEFAULT_DONORS</span></code></a> and
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_ACCEPTORS" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_ACCEPTORS"><code class="xref py py-attr docutils literal"><span class="pre">DEFAULT_ACCEPTORS</span></code></a> values.
 Available values: &#8220;CHARMM27&#8221;, &#8220;GLYCAM06&#8221;, &#8220;other&#8221; [&#8220;CHARMM27&#8221;]</p>
 </dd>
 <dt><em>donors</em></dt>
 <dd><p class="first last">Extra H donor atom types (in addition to those in
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_DONORS" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_DONORS"><tt class="xref py py-attr docutils literal"><span class="pre">DEFAULT_DONORS</span></tt></a>), must be a sequence.</p>
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_DONORS" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_DONORS"><code class="xref py py-attr docutils literal"><span class="pre">DEFAULT_DONORS</span></code></a>), must be a sequence.</p>
 </dd>
 <dt><em>acceptors</em></dt>
 <dd><p class="first last">Extra H acceptor atom types (in addition to those in
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_ACCEPTORS" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_ACCEPTORS"><tt class="xref py py-attr docutils literal"><span class="pre">DEFAULT_ACCEPTORS</span></tt></a>), must be a sequence.</p>
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_ACCEPTORS" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_ACCEPTORS"><code class="xref py py-attr docutils literal"><span class="pre">DEFAULT_ACCEPTORS</span></code></a>), must be a sequence.</p>
 </dd>
 <dt><em>start</em></dt>
-<dd><p class="first last">starting frame-index for analysis, <tt class="docutils literal"><span class="pre">None</span></tt> is the first one, 0.
+<dd><p class="first last">starting frame-index for analysis, <code class="docutils literal"><span class="pre">None</span></code> is the first one, 0.
 <em>start</em> and <em>stop</em> are 0-based frame indices and are used to slice
-the trajectory (if supported) [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+the trajectory (if supported) [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>stop</em></dt>
-<dd><p class="first last">last trajectory frame for analysis, <tt class="docutils literal"><span class="pre">None</span></tt> is the last one [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">last trajectory frame for analysis, <code class="docutils literal"><span class="pre">None</span></code> is the last one [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>step</em></dt>
-<dd><p class="first last">read every <em>step</em> between <em>start</em> and <em>stop</em>, <tt class="docutils literal"><span class="pre">None</span></tt> selects 1.
+<dd><p class="first last">read every <em>step</em> between <em>start</em> and <em>stop</em>, <code class="docutils literal"><span class="pre">None</span></code> selects 1.
 Note that not all trajectory readers perform well with a step different
-from 1 [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+from 1 [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>verbose</em></dt>
-<dd><p class="first last">If set to <tt class="docutils literal"><span class="pre">True</span></tt> enables per-frame debug logging. This is disabled
+<dd><p class="first last">If set to <code class="docutils literal"><span class="pre">True</span></code> enables per-frame debug logging. This is disabled
 by default because it generates a very large amount of output in
 the log file. (Note that a logger must have been started to see
-the output, e.g. using <a class="reference internal" href="../lib/log.html#MDAnalysis.start_logging" title="MDAnalysis.start_logging"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.start_logging()</span></tt></a>.)</p>
+the output, e.g. using <a class="reference internal" href="../lib/log.html#MDAnalysis.start_logging" title="MDAnalysis.start_logging"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.start_logging()</span></code></a>.)</p>
 </dd>
 <dt><em>detect_hydrogens</em></dt>
 <dd><p class="first last">Determine the algorithm to find hydrogens connected to donor
@@ -564,15 +567,16 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">SelectionError</span></tt> is raised for each static selection without
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">SelectionError</span></code> is raised for each static selection without
 the required donors and/or acceptors.</p>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>New <em>verbose</em> keyword (and per-frame debug logging disabled by
-default).<p>New <em>detect_hydrogens</em> keyword to switch between two different
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>New <em>verbose</em> keyword (and per-frame debug logging disabled by
+default).</p>
+<p>New <em>detect_hydrogens</em> keyword to switch between two different
 algorithms to detect hydrogens bonded to donor. &#8220;distance&#8221; is a new,
 rigorous distance search within the residue of the donor atom,
 &#8220;heuristic&#8221; is the previous list scan (improved with an additional
@@ -580,32 +584,35 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 <p>New <em>forcefield</em> keyword to switch between different values of
 DEFAULT_DONORS/ACCEPTORS to accomodate different force fields.
 Also has an option &#8220;other&#8221; for no default values.</p>
-</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>The new default for <em>update_selection1</em> and <em>update_selection2</em> is now
-<tt class="docutils literal"><span class="pre">True</span></tt> (see <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/138">Issue 138</a>). Set to <tt class="docutils literal"><span class="pre">False</span></tt> if your selections only
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>The new default for <em>update_selection1</em> and <em>update_selection2</em> is now
+<code class="docutils literal"><span class="pre">True</span></code> (see <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/138">Issue 138</a>). Set to <code class="docutils literal"><span class="pre">False</span></code> if your selections only
 need to be determined once (will increase performance).</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>distance_type</em> to select between calculation between
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>distance_type</em> to select between calculation between
 heavy atoms or hydrogen-acceptor. It defaults to the previous
 behavior (i.e. &#8220;hydrogen&#8221;).</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Initial checks for selections that potentially raise <tt class="xref py py-exc docutils literal"><span class="pre">SelectionError</span></tt>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Initial checks for selections that potentially raise <code class="xref py py-exc docutils literal"><span class="pre">SelectionError</span></code>.</p>
+</div>
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timesteps">
-<tt class="descname">timesteps</tt><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timesteps" title="Permalink to this definition">¶</a></dt>
+<code class="descname">timesteps</code><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timesteps" title="Permalink to this definition">¶</a></dt>
 <dd><p>List of the times of each timestep. This can be used together with
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><tt class="xref py py-attr docutils literal"><span class="pre">timeseries</span></tt></a> to find the specific time point
-of a hydrogen bond existence, or see <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table"><tt class="xref py py-attr docutils literal"><span class="pre">table</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><code class="xref py py-attr docutils literal"><span class="pre">timeseries</span></code></a> to find the specific time point
+of a hydrogen bond existence, or see <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table"><code class="xref py py-attr docutils literal"><span class="pre">table</span></code></a>.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries">
-<tt class="descname">timeseries</tt><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="Permalink to this definition">¶</a></dt>
+<code class="descname">timeseries</code><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="Permalink to this definition">¶</a></dt>
 <dd><p>Results of the hydrogen bond analysis, stored for each frame. In
 the following description, # indicates comments that are not
 part of the output:</p>
-<div class="highlight-python"><pre>results = [
+<div class="highlight-python"><div class="highlight"><pre>results = [
     [ # frame 1
        [ # hbond 1
           &lt;donor index&gt;, &lt;acceptor index&gt;, &lt;donor string&gt;, &lt;acceptor string&gt;, &lt;distance&gt;, &lt;angle&gt;
@@ -619,26 +626,27 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
       [ ... ], [ ... ], ...
     ],
     ...
-]</pre>
+]
+</pre></div>
 </div>
 <p>The time of each step is not stored with each hydrogen bond frame but in
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timesteps" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timesteps"><tt class="xref py py-attr docutils literal"><span class="pre">timesteps</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timesteps" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timesteps"><code class="xref py py-attr docutils literal"><span class="pre">timesteps</span></code></a>.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <em>index</em> is a 1-based index. To get the <tt class="xref py py-attr docutils literal"><span class="pre">Atom.index</span></tt> (the
+<p class="last">The <em>index</em> is a 1-based index. To get the <code class="xref py py-attr docutils literal"><span class="pre">Atom.index</span></code> (the
 0-based index typically used in MDAnalysis simply subtract 1. For
-instance, to find an atom in <tt class="xref py py-attr docutils literal"><span class="pre">Universe.atoms</span></tt> by <em>index</em> one
-would use <tt class="docutils literal"><span class="pre">u.atoms[index-1]</span></tt>.</p>
+instance, to find an atom in <code class="xref py py-attr docutils literal"><span class="pre">Universe.atoms</span></code> by <em>index</em> one
+would use <code class="docutils literal"><span class="pre">u.atoms[index-1]</span></code>.</p>
 </div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table">
-<tt class="descname">table</tt><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table" title="Permalink to this definition">¶</a></dt>
+<code class="descname">table</code><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table" title="Permalink to this definition">¶</a></dt>
 <dd><p>A normalised table of the data in
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><tt class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></tt></a>, generated by
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table"><tt class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis.generate_table()</span></tt></a>. It is a
-<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></tt></a> with the following columns:</p>
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></code></a>, generated by
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table"><code class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis.generate_table()</span></code></a>. It is a
+<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></code></a> with the following columns:</p>
 <blockquote>
 <div><ol class="arabic simple" start="0">
 <li>&#8220;time&#8221;</li>
@@ -655,46 +663,47 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </ol>
 </div></blockquote>
 <p>It takes up more space than
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><tt class="xref py py-attr docutils literal"><span class="pre">timeseries</span></tt></a> but it is easier to
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><code class="xref py py-attr docutils literal"><span class="pre">timeseries</span></code></a> but it is easier to
 analyze and to import into databases (e.g. using <a class="reference external" href="http://pypi.python.org/pypi/RecSQL">recsql</a>).</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <em>index</em> is a 1-based index. To get the <tt class="xref py py-attr docutils literal"><span class="pre">Atom.index</span></tt> (the
+<p class="last">The <em>index</em> is a 1-based index. To get the <code class="xref py py-attr docutils literal"><span class="pre">Atom.index</span></code> (the
 0-based index typically used in MDAnalysis simply subtract 1. For
-instance, to find an atom in <tt class="xref py py-attr docutils literal"><span class="pre">Universe.atoms</span></tt> by <em>index</em> one
-would use <tt class="docutils literal"><span class="pre">u.atoms[index-1]</span></tt>.</p>
+instance, to find an atom in <code class="xref py py-attr docutils literal"><span class="pre">Universe.atoms</span></code> by <em>index</em> one
+would use <code class="docutils literal"><span class="pre">u.atoms[index-1]</span></code>.</p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens">
-<tt class="descname">_get_bonded_hydrogens</tt><big>(</big><em>atom</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis._get_bonded_hydrogens"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_get_bonded_hydrogens</code><span class="sig-paren">(</span><em>atom</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis._get_bonded_hydrogens"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens" title="Permalink to this definition">¶</a></dt>
 <dd><p>Find hydrogens bonded to <em>atom</em>.</p>
 <p>This method is typically not called by a user but it is documented to
 facilitate understanding of the internals of
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis"><tt class="xref py py-class docutils literal"><span class="pre">HydrogenBondAnalysis</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis"><code class="xref py py-class docutils literal"><span class="pre">HydrogenBondAnalysis</span></code></a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">list of hydrogens (can be a
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>) or empty list
-<tt class="docutils literal"><span class="pre">[]</span></tt> if none were found.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">list of hydrogens (can be a
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>) or empty list
+<code class="docutils literal"><span class="pre">[]</span></code> if none were found.</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist"><tt class="xref py py-meth docutils literal"><span class="pre">_get_bonded_hydrogens_dist()</span></tt></a> and <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list"><tt class="xref py py-meth docutils literal"><span class="pre">_get_bonded_hydrogens_list()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist"><code class="xref py py-meth docutils literal"><span class="pre">_get_bonded_hydrogens_dist()</span></code></a> and <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list"><code class="xref py py-meth docutils literal"><span class="pre">_get_bonded_hydrogens_list()</span></code></a></p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>Can switch algorithm by using the <em>detect_hydrogens</em> keyword to the
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>Can switch algorithm by using the <em>detect_hydrogens</em> keyword to the
 constructor. <em>kwargs</em> can be used to supply arguments for algorithm.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist">
-<tt class="descname">_get_bonded_hydrogens_dist</tt><big>(</big><em>atom</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis._get_bonded_hydrogens_dist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_get_bonded_hydrogens_dist</code><span class="sig-paren">(</span><em>atom</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis._get_bonded_hydrogens_dist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist" title="Permalink to this definition">¶</a></dt>
 <dd><p>Find hydrogens bonded within <em>cutoff</em> to <em>atom</em>.</p>
 <ul class="simple">
 <li>hydrogens are detected by either name (&#8220;H*&#8221;, &#8220;[123]H*&#8221;) or type
@@ -703,68 +712,78 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 <li>The distance from <em>atom</em> is calculated for all hydrogens in the
 residue and only those within a cutoff are kept. The cutoff depends
 on the heavy atom (more precisely, on its element, which is taken as
-the first letter of its name <tt class="docutils literal"><span class="pre">atom.name[0]</span></tt>) and is parameterized
-in <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov"><tt class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.r_cov</span></tt></a>. If no match is found then the
+the first letter of its name <code class="docutils literal"><span class="pre">atom.name[0]</span></code>) and is parameterized
+in <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov"><code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.r_cov</span></code></a>. If no match is found then the
 default of 1.5 Å is used.</li>
 </ul>
 <p>The performance of this implementation could be improved once the
 topology always contains bonded information; it currently uses the
 selection parser with an &#8220;around&#8221; selection.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list">
-<tt class="descname">_get_bonded_hydrogens_list</tt><big>(</big><em>atom</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis._get_bonded_hydrogens_list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_get_bonded_hydrogens_list</code><span class="sig-paren">(</span><em>atom</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis._get_bonded_hydrogens_list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list" title="Permalink to this definition">¶</a></dt>
 <dd><p>Find &#8220;bonded&#8221; hydrogens to the donor <em>atom</em>.</p>
 <p>At the moment this relies on the <strong>assumption</strong> that the
 hydrogens are listed directly after the heavy atom in the
 topology. If this is not the case then this function will
 fail.</p>
-<p>Hydrogens are detected by name <tt class="docutils literal"><span class="pre">H*</span></tt>, <tt class="docutils literal"><span class="pre">[123]H*</span></tt> and they have to be
+<p>Hydrogens are detected by name <code class="docutils literal"><span class="pre">H*</span></code>, <code class="docutils literal"><span class="pre">[123]H*</span></code> and they have to be
 within a maximum distance from the heavy atom. The cutoff distance
 depends on the heavy atom and is parameterized in
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov"><tt class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.r_cov</span></tt></a>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6.</span></p>
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov"><code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.r_cov</span></code></a>.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>Added detection of <code class="docutils literal"><span class="pre">[123]H</span></code> and additional check that a
+selected hydrogen is bonded to the donor atom (i.e. its
+distance to the donor is less than the covalent radius
+stored in <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov"><code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.r_cov</span></code></a> or the default
+1.5 Å).</p>
+<p>Changed name to
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_list"><code class="xref py py-meth docutils literal"><span class="pre">_get_bonded_hydrogens_list()</span></code></a>
+and added <em>kwargs</em> so that it can be used instead of
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis._get_bonded_hydrogens_dist"><code class="xref py py-meth docutils literal"><span class="pre">_get_bonded_hydrogens_dist()</span></code></a>.</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_ACCEPTORS">
-<tt class="descname">DEFAULT_ACCEPTORS</tt><em class="property"> = {'GLYCAM06': ('SM', 'OH', 'NT', 'O', 'N', 'OY', 'OW', 'OS', 'O2'), 'other': (), 'CHARMM27': ('OH', 'OG', 'OD1', 'OD2', 'OG1', 'O', 'ND1', 'NE2', 'OE2', 'OW', 'SG', 'OE1', 'OH2', 'SD')}</em><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_ACCEPTORS" title="Permalink to this definition">¶</a></dt>
+<code class="descname">DEFAULT_ACCEPTORS</code><em class="property"> = {'GLYCAM06': ('SM', 'OH', 'NT', 'O', 'N', 'OY', 'OW', 'OS', 'O2'), 'other': (), 'CHARMM27': ('OH', 'OG', 'OD1', 'OD2', 'OG1', 'O', 'ND1', 'NE2', 'OE2', 'OW', 'SG', 'OE1', 'OH2', 'SD')}</em><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_ACCEPTORS" title="Permalink to this definition">¶</a></dt>
 <dd><p>default atom names that are treated as hydrogen <em>acceptors</em>
-(see <a class="reference internal" href="#default-atom-names-for-hydrogen-bonding-analysis"><em>Default heavy atom names for CHARMM27 force field.</em></a>)
+(see <a class="reference internal" href="#default-atom-names-for-hydrogen-bonding-analysis"><span>Default heavy atom names for CHARMM27 force field.</span></a>)
 Use the keyword <em>acceptors</em> to add a list of additional acceptor names.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_DONORS">
-<tt class="descname">DEFAULT_DONORS</tt><em class="property"> = {'GLYCAM06': ('OW', 'N3', 'NT', 'OH', 'N'), 'other': (), 'CHARMM27': ('OH', 'OG', 'NE2', 'OG1', 'NE', 'N', 'ND1', 'NZ', 'NH1', 'NH2', 'OW', 'ND2', 'SG', 'OH2', 'NE1')}</em><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_DONORS" title="Permalink to this definition">¶</a></dt>
+<code class="descname">DEFAULT_DONORS</code><em class="property"> = {'GLYCAM06': ('OW', 'N3', 'NT', 'OH', 'N'), 'other': (), 'CHARMM27': ('OH', 'OG', 'NE2', 'OG1', 'NE', 'N', 'ND1', 'NZ', 'NH1', 'NH2', 'OW', 'ND2', 'SG', 'OH2', 'NE1')}</em><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.DEFAULT_DONORS" title="Permalink to this definition">¶</a></dt>
 <dd><p>Use the keyword <em>donors</em> to add a list of additional donor names.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.calc_angle">
-<tt class="descname">calc_angle</tt><big>(</big><em>d</em>, <em>h</em>, <em>a</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.calc_angle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.calc_angle" title="Permalink to this definition">¶</a></dt>
+<code class="descname">calc_angle</code><span class="sig-paren">(</span><em>d</em>, <em>h</em>, <em>a</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.calc_angle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.calc_angle" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate the angle (in degrees) between two atoms with H at apex.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.calc_eucl_distance">
-<tt class="descname">calc_eucl_distance</tt><big>(</big><em>a1</em>, <em>a2</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.calc_eucl_distance"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.calc_eucl_distance" title="Permalink to this definition">¶</a></dt>
+<code class="descname">calc_eucl_distance</code><span class="sig-paren">(</span><em>a1</em>, <em>a2</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.calc_eucl_distance"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.calc_eucl_distance" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate the Euclidean distance between two atoms.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.count_by_time">
-<tt class="descname">count_by_time</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.count_by_time"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.count_by_time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">count_by_time</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.count_by_time"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.count_by_time" title="Permalink to this definition">¶</a></dt>
 <dd><p>Counts the number of hydrogen bonds per timestep.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">a class:<cite>numpy.recarray</cite></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">a class:<cite>numpy.recarray</cite></td>
 </tr>
 </tbody>
 </table>
@@ -772,10 +791,10 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.count_by_type">
-<tt class="descname">count_by_type</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.count_by_type"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.count_by_type" title="Permalink to this definition">¶</a></dt>
+<code class="descname">count_by_type</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.count_by_type"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.count_by_type" title="Permalink to this definition">¶</a></dt>
 <dd><p>Counts the frequency of hydrogen bonds of a specific type.</p>
-<p>Processes <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><tt class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></tt></a> and returns
-a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></tt></a> containing atom indices, residue
+<p>Processes <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></code></a> and returns
+a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></code></a> containing atom indices, residue
 names, residue numbers (for donors and acceptors) and the
 fraction of the total time during which the hydrogen bond was
 detected.</p>
@@ -783,7 +802,7 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">a class:<cite>numpy.recarray</cite></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">a class:<cite>numpy.recarray</cite></td>
 </tr>
 </tbody>
 </table>
@@ -791,10 +810,10 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table">
-<tt class="descname">generate_table</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.generate_table"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table" title="Permalink to this definition">¶</a></dt>
+<code class="descname">generate_table</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.generate_table"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table" title="Permalink to this definition">¶</a></dt>
 <dd><p>Generate a normalised table of the results.</p>
-<p>The table is stored as a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></tt></a> in the
-attribute <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table"><tt class="xref py py-attr docutils literal"><span class="pre">table</span></tt></a> and can be used
+<p>The table is stored as a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></code></a> in the
+attribute <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table"><code class="xref py py-attr docutils literal"><span class="pre">table</span></code></a> and can be used
 with e.g. <a class="reference external" href="http://pypi.python.org/pypi/RecSQL">recsql</a>.</p>
 <dl class="docutils">
 <dt>Columns:</dt>
@@ -817,8 +836,8 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov">
-<tt class="descname">r_cov</tt><em class="property"> = defaultdict(&lt;function &lt;lambda&gt; at 0x10a4f1140&gt;, {'P': 1.58, 'S': 1.55, 'O': 1.31, 'N': 1.31})</em><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov" title="Permalink to this definition">¶</a></dt>
-<dd><p>A <a class="reference external" href="http://docs.python.org/library/collections.html#collections.defaultdict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">collections.defaultdict</span></tt></a> of covalent radii of common donors
+<code class="descname">r_cov</code><em class="property"> = defaultdict(&lt;function &lt;lambda&gt; at 0x2af820fdac08&gt;, {'P': 1.58, 'S': 1.55, 'O': 1.31, 'N': 1.31})</em><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.r_cov" title="Permalink to this definition">¶</a></dt>
+<dd><p>A <a class="reference external" href="http://docs.python.org/library/collections.html#collections.defaultdict" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">collections.defaultdict</span></code></a> of covalent radii of common donors
 (used in :meth`_get_bonded_hydrogens_list` to check if a hydrogen is
 sufficiently close to its donor heavy atom). Values are stored for
 N, O, P, and S. Any other heavy atoms are assumed to have hydrogens
@@ -827,58 +846,60 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Analyze trajectory and produce timeseries.</p>
 <p>Stores the hydrogen bond data per frame as
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><tt class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></tt></a> (see there for output
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></code></a> (see there for output
 format).</p>
 <p>The method accepts a number of keywords, amongst them <em>quiet</em> (default
-<tt class="docutils literal"><span class="pre">False</span></tt>), which silences the porgress output (see
-<a class="reference internal" href="../lib/log.html#MDAnalysis.lib.log.ProgressMeter" title="MDAnalysis.lib.log.ProgressMeter"><tt class="xref py py-class docutils literal"><span class="pre">ProgressMeter</span></tt></a>) and <em>verbose</em> (which can
+<code class="docutils literal"><span class="pre">False</span></code>), which silences the porgress output (see
+<a class="reference internal" href="../lib/log.html#MDAnalysis.lib.log.ProgressMeter" title="MDAnalysis.lib.log.ProgressMeter"><code class="xref py py-class docutils literal"><span class="pre">ProgressMeter</span></code></a>) and <em>verbose</em> (which can
 be used to change the value provided with the class constructor).</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table"><tt class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis.generate_table()</span></tt></a> for processing
+<p class="last"><a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.generate_table"><code class="xref py py-meth docutils literal"><span class="pre">HydrogenBondAnalysis.generate_table()</span></code></a> for processing
 the data into a different format.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>Results are not returned, only stored in
-<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><tt class="xref py py-attr docutils literal"><span class="pre">timeseries</span></tt></a> and duplicate hydrogen bonds
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>Results are not returned, only stored in
+<a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><code class="xref py py-attr docutils literal"><span class="pre">timeseries</span></code></a> and duplicate hydrogen bonds
 are removed from output (can be suppressed with <em>remove_duplicates</em> =
-<tt class="docutils literal"><span class="pre">False</span></tt>)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Accept <em>quiet</em> keyword. Analysis will now proceed through frames even if
+<code class="docutils literal"><span class="pre">False</span></code>)</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Accept <em>quiet</em> keyword. Analysis will now proceed through frames even if
 no donors or acceptors were found in a particular frame.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.save_table">
-<tt class="descname">save_table</tt><big>(</big><em>filename='hbond_table.pickle'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.save_table"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.save_table" title="Permalink to this definition">¶</a></dt>
-<dd><p>Saves <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table"><tt class="xref py py-attr docutils literal"><span class="pre">table</span></tt></a> to a pickled file.</p>
+<code class="descname">save_table</code><span class="sig-paren">(</span><em>filename='hbond_table.pickle'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.save_table"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.save_table" title="Permalink to this definition">¶</a></dt>
+<dd><p>Saves <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.table"><code class="xref py py-attr docutils literal"><span class="pre">table</span></code></a> to a pickled file.</p>
 <p>Load with</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">cPickle</span>
 <span class="n">table</span> <span class="o">=</span> <span class="n">cPickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
 </pre></div>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference external" href="http://docs.python.org/library/pickle.html#module-cPickle" title="(in Python v2.7)"><tt class="xref py py-mod docutils literal"><span class="pre">cPickle</span></tt></a> module and <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></tt></a></p>
+<p class="last"><a class="reference external" href="http://docs.python.org/library/pickle.html#module-cPickle" title="(in Python v2.7)"><code class="xref py py-mod docutils literal"><span class="pre">cPickle</span></code></a> module and <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></code></a></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timesteps_by_type">
-<tt class="descname">timesteps_by_type</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.timesteps_by_type"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timesteps_by_type" title="Permalink to this definition">¶</a></dt>
+<code class="descname">timesteps_by_type</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html#HydrogenBondAnalysis.timesteps_by_type"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timesteps_by_type" title="Permalink to this definition">¶</a></dt>
 <dd><p>Frames during which each hydrogen bond existed, sorted by hydrogen bond.</p>
-<p>Processes <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><tt class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></tt></a> and returns
-a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></tt></a> containing atom indices, residue
+<p>Processes <a class="reference internal" href="#MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries" title="MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis.timeseries"><code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondAnalysis.timeseries</span></code></a> and returns
+a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></code></a> containing atom indices, residue
 names, residue numbers (for donors and acceptors) and a list
 of timesteps at which the hydrogen bond was detected.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">a class:<cite>numpy.recarray</cite></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">a class:<cite>numpy.recarray</cite></td>
 </tr>
 </tbody>
 </table>
@@ -895,7 +916,7 @@ <h2>3.2.1.4. Classes<a class="headerlink" href="#classes" title="Permalink to th
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -910,11 +931,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="psa.html" title="3.1.5. Calculating path similarity — MDAnalysis.analysis.psa"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -924,7 +945,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/hbond_autocorrel.html b/package/doc/html/documentation_pages/analysis/hbond_autocorrel.html
index 564651ce16f..1f4876bc8e8 100644
--- a/package/doc/html/documentation_pages/analysis/hbond_autocorrel.html
+++ b/package/doc/html/documentation_pages/analysis/hbond_autocorrel.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.2.2. Hydrogen bond autocorrelation — MDAnalysis.analysis.hbonds.hbond_autocorrel &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.2.2. Hydrogen bond autocorrelation — MDAnalysis.analysis.hbonds.hbond_autocorrel &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
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@@ -16,7 +14,7 @@
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       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="3.3.1. Generation and Analysis of HOLE pore profiles — MDAnalysis.analysis.hole" href="hole.html" />
     <link rel="prev" title="3.2.1. Hydrogen Bond analysis — MDAnalysis.analysis.hbonds.hbond_analysis" href="hbond_analysis.html" /> 
   </head>
-  <body>
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
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@@ -51,18 +49,18 @@ <h3>Navigation</h3>
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           <a href="hbond_analysis.html" title="3.2.1. Hydrogen Bond analysis — MDAnalysis.analysis.hbonds.hbond_analysis"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.2.2. Hydrogen bond autocorrelation &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_autocorrel</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.2.2. Hydrogen bond autocorrelation &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_autocorrel</span></code></a><ul>
 <li><a class="reference internal" href="#description">3.2.2.1. Description</a></li>
 <li><a class="reference internal" href="#input">3.2.2.2. Input</a></li>
 <li><a class="reference internal" href="#output">3.2.2.3. Output</a></li>
@@ -73,16 +71,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="hbond_analysis.html"
-                        title="previous chapter">3.2.1. Hydrogen Bond analysis &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_analysis</span></tt></a></p>
+                        title="previous chapter">3.2.1. Hydrogen Bond analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_analysis</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="hole.html"
-                        title="next chapter">3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.hole</span></tt></a></p>
-  <h3>This Page</h3>
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+                        title="next chapter">3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.hole</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
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+      <li><a href="../../_sources/documentation_pages/analysis/hbond_autocorrel.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -101,10 +101,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.hbonds.hbond_autocorrel"></span><div class="section" id="hydrogen-bond-autocorrelation-mdanalysis-analysis-hbonds-hbond-autocorrel">
-<h1>3.2.2. Hydrogen bond autocorrelation &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.hbonds.hbond_autocorrel" title="MDAnalysis.analysis.hbonds.hbond_autocorrel"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_autocorrel</span></tt></a><a class="headerlink" href="#hydrogen-bond-autocorrelation-mdanalysis-analysis-hbonds-hbond-autocorrel" title="Permalink to this headline">¶</a></h1>
+<h1>3.2.2. Hydrogen bond autocorrelation &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.hbonds.hbond_autocorrel" title="MDAnalysis.analysis.hbonds.hbond_autocorrel"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_autocorrel</span></code></a><a class="headerlink" href="#hydrogen-bond-autocorrelation-mdanalysis-analysis-hbonds-hbond-autocorrel" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -117,8 +117,9 @@ <h1>3.2.2. Hydrogen bond autocorrelation &#8212; <a class="reference internal" h
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
 <div class="section" id="description">
 <h2>3.2.2.1. Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
 <p>Calculates the time autocorrelation function, <span class="math">\(C_x(t)\)</span>, for the hydrogen
@@ -196,8 +197,8 @@ <h2>3.2.2.3. Output<a class="headerlink" href="#output" title="Permalink to this
 <li><p class="first"><em>estimate</em> Estimated values generated by the calculated fit.</p>
 </li>
 </ul>
-<p>The <em>results</em> and <em>time</em> values are only filled after the <tt class="xref py py-meth docutils literal"><span class="pre">run()</span></tt> method,
-<em>fit</em>, <em>tau</em> and <em>estimate</em> are filled after the <tt class="xref py py-meth docutils literal"><span class="pre">solve()</span></tt> method has been
+<p>The <em>results</em> and <em>time</em> values are only filled after the <code class="xref py py-meth docutils literal"><span class="pre">run()</span></code> method,
+<em>fit</em>, <em>tau</em> and <em>estimate</em> are filled after the <code class="xref py py-meth docutils literal"><span class="pre">solve()</span></code> method has been
 used.</p>
 </div>
 <div class="section" id="examples">
@@ -223,13 +224,13 @@ <h2>3.2.2.4. Examples<a class="headerlink" href="#examples" title="Permalink to
 </div>
 <dl class="class">
 <dt id="MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.hbonds.hbond_autocorrel.</tt><tt class="descname">HydrogenBondAutoCorrel</tt><big>(</big><em>universe</em>, <em>hydrogens=None</em>, <em>acceptors=None</em>, <em>donors=None</em>, <em>bond_type=None</em>, <em>exclusions=None</em>, <em>angle_crit=130.0</em>, <em>dist_crit=3.0</em>, <em>sample_time=100</em>, <em>time_cut=None</em>, <em>nruns=1</em>, <em>nsamples=50</em>, <em>pbc=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html#HydrogenBondAutoCorrel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.hbonds.hbond_autocorrel.</code><code class="descname">HydrogenBondAutoCorrel</code><span class="sig-paren">(</span><em>universe</em>, <em>hydrogens=None</em>, <em>acceptors=None</em>, <em>donors=None</em>, <em>bond_type=None</em>, <em>exclusions=None</em>, <em>angle_crit=130.0</em>, <em>dist_crit=3.0</em>, <em>sample_time=100</em>, <em>time_cut=None</em>, <em>nruns=1</em>, <em>nsamples=50</em>, <em>pbc=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html#HydrogenBondAutoCorrel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel" title="Permalink to this definition">¶</a></dt>
 <dd><p>Perform a time autocorrelation of the hydrogen bonds in the system.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">The MDA universe</p>
 </dd>
@@ -253,7 +254,7 @@ <h2>3.2.2.4. Examples<a class="headerlink" href="#examples" title="Permalink to
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>exclusions</em></dt>
 <dd><p class="first last">Indices of Hydrogen-Acceptor pairs to be excluded.
 With nH and nA Hydrogens and Acceptors, a (nH x nA) array of distances
@@ -278,7 +279,7 @@ <h2>3.2.2.4. Examples<a class="headerlink" href="#examples" title="Permalink to
 <dd><p class="first last">Within each run, the number of frames to analyse [50]</p>
 </dd>
 <dt><em>pbc</em></dt>
-<dd><p class="first last">Whether to consider periodic boundaries in calculations [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">Whether to consider periodic boundaries in calculations [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -287,13 +288,13 @@ <h2>3.2.2.4. Examples<a class="headerlink" href="#examples" title="Permalink to
 </table>
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel.run">
-<tt class="descname">run</tt><big>(</big><em>force=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html#HydrogenBondAutoCorrel.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>force=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html#HydrogenBondAutoCorrel.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Run all the required passes</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>force</em></dt>
 <dd><p class="first last">Will overwrite previous results if they exist</p>
 </dd>
@@ -306,14 +307,14 @@ <h2>3.2.2.4. Examples<a class="headerlink" href="#examples" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel.solve">
-<tt class="descname">solve</tt><big>(</big><em>p_guess=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html#HydrogenBondAutoCorrel.solve"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel.solve" title="Permalink to this definition">¶</a></dt>
+<code class="descname">solve</code><span class="sig-paren">(</span><em>p_guess=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html#HydrogenBondAutoCorrel.solve"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel.solve" title="Permalink to this definition">¶</a></dt>
 <dd><p>Fit results to an multi exponential decay and integrate to find
 characteristic time</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>p_guess</em></dt>
 <dd><p class="first last">Initial guess for the leastsq fit, must match the shape of the
 expected coefficients</p>
@@ -350,14 +351,14 @@ <h2>3.2.2.4. Examples<a class="headerlink" href="#examples" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel.save_results">
-<tt class="descname">save_results</tt><big>(</big><em>filename='hbond_autocorrel'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html#HydrogenBondAutoCorrel.save_results"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel.save_results" title="Permalink to this definition">¶</a></dt>
+<code class="descname">save_results</code><span class="sig-paren">(</span><em>filename='hbond_autocorrel'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html#HydrogenBondAutoCorrel.save_results"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel.save_results" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves the results to a numpy zipped array (.npz, see numpy.savez)</p>
 <p>This can be loaded using numpy.load(filename)</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">The desired filename [hbond_autocorrel]</p>
 </dd>
@@ -379,7 +380,7 @@ <h2>3.2.2.4. Examples<a class="headerlink" href="#examples" title="Permalink to
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -394,11 +395,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="hbond_analysis.html" title="3.2.1. Hydrogen Bond analysis — MDAnalysis.analysis.hbonds.hbond_analysis"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -408,7 +409,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/helanal.html b/package/doc/html/documentation_pages/analysis/helanal.html
index 35ebf524bed..becc9156d2e 100644
--- a/package/doc/html/documentation_pages/analysis/helanal.html
+++ b/package/doc/html/documentation_pages/analysis/helanal.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.5.2. HELANAL — analysis of protein helices &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.5.2. HELANAL — analysis of protein helices &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
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-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
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     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="3.6.1. Generating densities from trajectories — MDAnalysis.analysis.density" href="density.html" />
     <link rel="prev" title="3.5.1. Elastic network analysis of MD trajectories — MDAnalysis.analysis.gnm" href="gnm.html" /> 
   </head>
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="gnm.html" title="3.5.1. Elastic network analysis of MD trajectories — MDAnalysis.analysis.gnm"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
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-      <div class="sphinxsidebar">
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         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -72,16 +70,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
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-                        title="previous chapter">3.5.1. Elastic network analysis of MD trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.gnm</span></tt></a></p>
+                        title="previous chapter">3.5.1. Elastic network analysis of MD trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.gnm</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="density.html"
-                        title="next chapter">3.6.1. Generating densities from trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.density</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/analysis/helanal.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">3.6.1. Generating densities from trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.density</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/analysis/helanal.txt"
+            rel="nofollow">Show Source</a></li>
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+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -100,7 +100,7 @@ <h3>Quick search</h3>
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+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.helanal"></span><div class="section" id="helanal-analysis-of-protein-helices">
 <h1>3.5.2. HELANAL &#8212; analysis of protein helices<a class="headerlink" href="#helanal-analysis-of-protein-helices" title="Permalink to this headline">¶</a></h1>
@@ -116,13 +116,13 @@ <h1>3.5.2. HELANAL &#8212; analysis of protein helices<a class="headerlink" href
 </tr>
 </tbody>
 </table>
-<p>The <a class="reference internal" href="#module-MDAnalysis.analysis.helanal" title="MDAnalysis.analysis.helanal"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.helanal</span></tt></a> module is a Python implementation of the
-<a class="reference external" href="http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html">HELANAL</a> algorithm <a class="reference internal" href="#bansal2000">[Bansal2000]</a> in <a class="reference external" href="http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.f">helanal.f</a>, which is also available
+<p>The <a class="reference internal" href="#module-MDAnalysis.analysis.helanal" title="MDAnalysis.analysis.helanal"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.helanal</span></code></a> module is a Python implementation of the
+<a class="reference external" href="http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html">HELANAL</a> algorithm <a class="reference internal" href="#bansal2000" id="id1">[Bansal2000]</a> in <a class="reference external" href="http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.f">helanal.f</a>, which is also available
 through the <a class="reference external" href="http://nucleix.mbu.iisc.ernet.in/helanal/helanal.shtml">HELANAL webserver</a>.</p>
-<p>Please cite the paper <a class="reference internal" href="#bansal2000">[Bansal2000]</a> (and possibly <a class="reference internal" href="#kumar1996">[Kumar1996]</a> and
-<a class="reference internal" href="#kumar1998">[Kumar1998]</a>) in published work when using
-<a class="reference internal" href="#MDAnalysis.analysis.helanal.helanal_trajectory" title="MDAnalysis.analysis.helanal.helanal_trajectory"><tt class="xref py py-mod docutils literal"><span class="pre">helanal_trajectory</span></tt></a> or
-<a class="reference internal" href="#MDAnalysis.analysis.helanal.helanal_main" title="MDAnalysis.analysis.helanal.helanal_main"><tt class="xref py py-mod docutils literal"><span class="pre">helanal_main</span></tt></a>.</p>
+<p>Please cite the paper <a class="reference internal" href="#bansal2000" id="id2">[Bansal2000]</a> (and possibly <a class="reference internal" href="#kumar1996" id="id3">[Kumar1996]</a> and
+<a class="reference internal" href="#kumar1998" id="id4">[Kumar1998]</a>) in published work when using
+<a class="reference internal" href="#MDAnalysis.analysis.helanal.helanal_trajectory" title="MDAnalysis.analysis.helanal.helanal_trajectory"><code class="xref py py-mod docutils literal"><span class="pre">helanal_trajectory</span></code></a> or
+<a class="reference internal" href="#MDAnalysis.analysis.helanal.helanal_main" title="MDAnalysis.analysis.helanal.helanal_main"><code class="xref py py-mod docutils literal"><span class="pre">helanal_main</span></code></a>.</p>
 <p><a class="reference external" href="http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html">HELANAL</a> quantifies the geometry of helices in proteins on the basis of their Cα
 atoms alone. It can extract the helices from the structure files and then
 characterises the overall geometry of each helix as being linear, curved or
@@ -141,7 +141,7 @@ <h2>3.5.2.1. Background<a class="headerlink" href="#background" title="Permalink
 <p><a class="reference external" href="http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html">HELANAL</a> can be used to characterize the geometry of helices with a minimum 9
 residues. The geometry of an alpha helix is characterized by computing local
 helix axes and local helix origins for four contiguous C-Alpha atoms, using the
-procedure of Sugeta and Miyazawa <a class="reference internal" href="#sugeta1967">[Sugeta1967]</a> and sliding this window over
+procedure of Sugeta and Miyazawa <a class="reference internal" href="#sugeta1967" id="id5">[Sugeta1967]</a> and sliding this window over
 the length of the helix in steps of one C-alpha atom.</p>
 <p>The angles between successive local helix axes can identify <em>local bends</em> or
 <em>kinks</em> as well as occurrence of <em>smooth curvature</em> in the helix. A matrix, whose
@@ -195,7 +195,7 @@ <h2>3.5.2.2. References<a class="headerlink" href="#references" title="Permalink
 <h2>3.5.2.3. Functions<a class="headerlink" href="#functions" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.analysis.helanal.helanal_trajectory">
-<tt class="descclassname">MDAnalysis.analysis.helanal.</tt><tt class="descname">helanal_trajectory</tt><big>(</big><em>universe</em>, <em>selection='name CA'</em>, <em>start=None</em>, <em>end=None</em>, <em>begin=None</em>, <em>finish=None</em>, <em>matrix_filename='bending_matrix.dat'</em>, <em>origin_pdbfile='origin.pdb'</em>, <em>summary_filename='summary.txt'</em>, <em>screw_filename='screw.xvg'</em>, <em>tilt_filename='local_tilt.xvg'</em>, <em>fitted_tilt_filename='fit_tilt.xvg'</em>, <em>bend_filename='local_bend.xvg'</em>, <em>twist_filename='unit_twist.xvg'</em>, <em>prefix='helanal_'</em>, <em>ref_axis=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/helanal.html#helanal_trajectory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.helanal.helanal_trajectory" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.helanal.</code><code class="descname">helanal_trajectory</code><span class="sig-paren">(</span><em>universe</em>, <em>selection='name CA'</em>, <em>start=None</em>, <em>end=None</em>, <em>begin=None</em>, <em>finish=None</em>, <em>matrix_filename='bending_matrix.dat'</em>, <em>origin_pdbfile='origin.pdb'</em>, <em>summary_filename='summary.txt'</em>, <em>screw_filename='screw.xvg'</em>, <em>tilt_filename='local_tilt.xvg'</em>, <em>fitted_tilt_filename='fit_tilt.xvg'</em>, <em>bend_filename='local_bend.xvg'</em>, <em>twist_filename='unit_twist.xvg'</em>, <em>prefix='helanal_'</em>, <em>ref_axis=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/helanal.html#helanal_trajectory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.helanal.helanal_trajectory" title="Permalink to this definition">¶</a></dt>
 <dd><p>Perform <a class="reference external" href="http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html">HELANAL</a> helix analysis on all frames in <em>universe</em>.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
@@ -206,16 +206,16 @@ <h2>3.5.2.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a></p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a></p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>selection</em></dt>
-<dd><p class="first last">selection string that selects Calpha atoms [<tt class="docutils literal"><span class="pre">&quot;name</span> <span class="pre">CA&quot;</span></tt>]</p>
+<dd><p class="first last">selection string that selects Calpha atoms [<code class="docutils literal"><span class="pre">&quot;name</span> <span class="pre">CA&quot;</span></code>]</p>
 </dd>
 <dt><em>start</em></dt>
 <dd><p class="first last">start residue</p>
@@ -224,50 +224,50 @@ <h2>3.5.2.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 <dd><p class="first last">end residue</p>
 </dd>
 <dt><em>begin</em></dt>
-<dd><p class="first last">start analysing for time (ps) &gt;= <em>begin</em>; <tt class="docutils literal"><span class="pre">None</span></tt> starts from the
-beginning [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">start analysing for time (ps) &gt;= <em>begin</em>; <code class="docutils literal"><span class="pre">None</span></code> starts from the
+beginning [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>finish</em></dt>
-<dd><p class="first last">stop analysis for time (ps) =&lt; <em>finish</em>; <tt class="docutils literal"><span class="pre">None</span></tt> goes to the
-end of the trajectory [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">stop analysis for time (ps) =&lt; <em>finish</em>; <code class="docutils literal"><span class="pre">None</span></code> goes to the
+end of the trajectory [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>matrix_filename</em></dt>
-<dd><p class="first last">Output file- bending matrix [<tt class="docutils literal"><span class="pre">&quot;bending_matrix.dat&quot;</span></tt>]</p>
+<dd><p class="first last">Output file- bending matrix [<code class="docutils literal"><span class="pre">&quot;bending_matrix.dat&quot;</span></code>]</p>
 </dd>
 <dt><em>origin_pdbfile</em></dt>
-<dd><p class="first last">Output file- origin pdb file [<tt class="docutils literal"><span class="pre">&quot;origin.pdb&quot;</span></tt>]</p>
+<dd><p class="first last">Output file- origin pdb file [<code class="docutils literal"><span class="pre">&quot;origin.pdb&quot;</span></code>]</p>
 </dd>
 <dt><em>summary_filename</em></dt>
-<dd><p class="first last">Output file- all of the basic data [<tt class="docutils literal"><span class="pre">&quot;summary.txt&quot;</span></tt>]</p>
+<dd><p class="first last">Output file- all of the basic data [<code class="docutils literal"><span class="pre">&quot;summary.txt&quot;</span></code>]</p>
 </dd>
 <dt><em>screw_filename</em></dt>
 <dd><p class="first last">Output file- local tilts of individual residues from 2 to n-1
-[<tt class="docutils literal"><span class="pre">&quot;screw.xvg&quot;</span></tt>]</p>
+[<code class="docutils literal"><span class="pre">&quot;screw.xvg&quot;</span></code>]</p>
 </dd>
 <dt><em>tilt_filename</em></dt>
 <dd><p class="first last">Output file- tilt of line of best fit applied to origin axes
-[<tt class="docutils literal"><span class="pre">&quot;local_tilt.xvg&quot;</span></tt>]</p>
+[<code class="docutils literal"><span class="pre">&quot;local_tilt.xvg&quot;</span></code>]</p>
 </dd>
 <dt><em>bend_filename</em></dt>
 <dd><p class="first last">Output file- local bend angles between successive local helix axes
-[<tt class="docutils literal"><span class="pre">&quot;local_bend.xvg&quot;</span></tt>]</p>
+[<code class="docutils literal"><span class="pre">&quot;local_bend.xvg&quot;</span></code>]</p>
 </dd>
 <dt><em>twist_filename</em></dt>
 <dd><p class="first last">Output file- local unit twist between successive helix turns
-[<tt class="docutils literal"><span class="pre">&quot;unit_twist.xvg&quot;</span></tt>]</p>
+[<code class="docutils literal"><span class="pre">&quot;unit_twist.xvg&quot;</span></code>]</p>
 </dd>
 <dt><em>prefix</em></dt>
-<dd><p class="first last">Prefix to add to all output file names; set to <tt class="docutils literal"><span class="pre">None</span></tt> to disable
-[<tt class="docutils literal"><span class="pre">&quot;helanal__&quot;</span></tt>]</p>
+<dd><p class="first last">Prefix to add to all output file names; set to <code class="docutils literal"><span class="pre">None</span></code> to disable
+[<code class="docutils literal"><span class="pre">&quot;helanal__&quot;</span></code>]</p>
 </dd>
 <dt><em>ref_axis</em></dt>
-<dd><p class="first last">Calculate tilt angle relative to the axis; if <tt class="docutils literal"><span class="pre">None</span></tt> then <tt class="docutils literal"><span class="pre">[0,0,1]</span></tt>
-is chosen [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">Calculate tilt angle relative to the axis; if <code class="docutils literal"><span class="pre">None</span></code> then <code class="docutils literal"><span class="pre">[0,0,1]</span></code>
+is chosen [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
 <dt>FinishTimeException</dt>
 <dd><p class="first last">If the specified finish time precedes the specified start time or current time stamp of trajectory object.</p>
 </dd>
@@ -280,7 +280,7 @@ <h2>3.5.2.3. Functions<a class="headerlink" href="#functions" title="Permalink t
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.helanal.helanal_main">
-<tt class="descclassname">MDAnalysis.analysis.helanal.</tt><tt class="descname">helanal_main</tt><big>(</big><em>pdbfile</em>, <em>selection='name CA'</em>, <em>start=None</em>, <em>end=None</em>, <em>ref_axis=None</em>, <em>permissive=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/helanal.html#helanal_main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.helanal.helanal_main" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.helanal.</code><code class="descname">helanal_main</code><span class="sig-paren">(</span><em>pdbfile</em>, <em>selection='name CA'</em>, <em>start=None</em>, <em>end=None</em>, <em>ref_axis=None</em>, <em>permissive=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/helanal.html#helanal_main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.helanal.helanal_main" title="Permalink to this definition">¶</a></dt>
 <dd><p>Simple HELANAL run on a single frame PDB/GRO.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
@@ -298,7 +298,7 @@ <h2>3.5.2.3. Functions<a class="headerlink" href="#functions" title="Permalink t
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -313,11 +313,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="gnm.html" title="3.5.1. Elastic network analysis of MD trajectories — MDAnalysis.analysis.gnm"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -327,7 +327,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/hole.html b/package/doc/html/documentation_pages/analysis/hole.html
index 373a529ae39..a24bc70fbde 100644
--- a/package/doc/html/documentation_pages/analysis/hole.html
+++ b/package/doc/html/documentation_pages/analysis/hole.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.3.1. Generation and Analysis of HOLE pore profiles — MDAnalysis.analysis.hole &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.3.1. Generation and Analysis of HOLE pore profiles — MDAnalysis.analysis.hole &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="3.3.2. Leaflet identification — MDAnalysis.analysis.leaflet" href="leaflet.html" />
     <link rel="prev" title="3.2.2. Hydrogen bond autocorrelation — MDAnalysis.analysis.hbonds.hbond_autocorrel" href="hbond_autocorrel.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="hbond_autocorrel.html" title="3.2.2. Hydrogen bond autocorrelation — MDAnalysis.analysis.hbonds.hbond_autocorrel"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.hole</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.hole</span></code></a><ul>
 <li><a class="reference internal" href="#examples">3.3.1.1. Examples</a><ul>
 <li><a class="reference internal" href="#single-structure">3.3.1.1.1. Single structure</a></li>
 <li><a class="reference internal" href="#trajectory">3.3.1.1.2. Trajectory</a></li>
@@ -78,16 +76,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="hbond_autocorrel.html"
-                        title="previous chapter">3.2.2. Hydrogen bond autocorrelation &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_autocorrel</span></tt></a></p>
+                        title="previous chapter">3.2.2. Hydrogen bond autocorrelation &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_autocorrel</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="leaflet.html"
-                        title="next chapter">3.3.2. Leaflet identification &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.leaflet</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/analysis/hole.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">3.3.2. Leaflet identification &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.leaflet</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/analysis/hole.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -106,10 +106,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.hole"></span><div class="section" id="generation-and-analysis-of-hole-pore-profiles-mdanalysis-analysis-hole">
-<h1>3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.hole" title="MDAnalysis.analysis.hole"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.hole</span></tt></a><a class="headerlink" href="#generation-and-analysis-of-hole-pore-profiles-mdanalysis-analysis-hole" title="Permalink to this headline">¶</a></h1>
+<h1>3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.hole" title="MDAnalysis.analysis.hole"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.hole</span></code></a><a class="headerlink" href="#generation-and-analysis-of-hole-pore-profiles-mdanalysis-analysis-hole" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -123,7 +123,7 @@ <h1>3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <a class="refer
 </tbody>
 </table>
 <p>With the help of this module, <a class="reference external" href="http://www.smartsci.uk/hole/">HOLE</a> can be run on frames in a trajectory. Data
-can be combined and analyzed. <a class="reference external" href="http://www.smartsci.uk/hole/">HOLE</a> <a class="reference internal" href="#smart1993">[Smart1993]</a> <a class="reference internal" href="#smart1996">[Smart1996]</a> must be installed
+can be combined and analyzed. <a class="reference external" href="http://www.smartsci.uk/hole/">HOLE</a> <a class="reference internal" href="#smart1993" id="id1">[Smart1993]</a> <a class="reference internal" href="#smart1996" id="id2">[Smart1996]</a> must be installed
 separately and can be obtained from <a class="reference external" href="http://www.smartsci.uk/hole/">http://www.smartsci.uk/hole/</a>.</p>
 <p class="rubric">References</p>
 <table class="docutils citation" frame="void" id="smart1993" rules="none">
@@ -166,8 +166,8 @@ <h3>3.3.1.1.2. Trajectory<a class="headerlink" href="#trajectory" title="Permali
 <span class="n">H</span><span class="o">.</span><span class="n">plot3D</span><span class="p">()</span>
 </pre></div>
 </div>
-<p>The profiles are available as the attribute <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj.profiles" title="MDAnalysis.analysis.hole.HOLEtraj.profiles"><tt class="xref py py-attr docutils literal"><span class="pre">HOLEtraj.profiles</span></tt></a>
-(<tt class="docutils literal"><span class="pre">H.profiles</span></tt> in the example) and are indexed by frame number but
+<p>The profiles are available as the attribute <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj.profiles" title="MDAnalysis.analysis.hole.HOLEtraj.profiles"><code class="xref py py-attr docutils literal"><span class="pre">HOLEtraj.profiles</span></code></a>
+(<code class="docutils literal"><span class="pre">H.profiles</span></code> in the example) and are indexed by frame number but
 can also be indexed by an arbitrary order parameter as shown in the
 next example.</p>
 </div>
@@ -175,7 +175,7 @@ <h3>3.3.1.1.2. Trajectory<a class="headerlink" href="#trajectory" title="Permali
 <h3>3.3.1.1.3. Trajectory with RMSD as order parameter<a class="headerlink" href="#trajectory-with-rmsd-as-order-parameter" title="Permalink to this headline">¶</a></h3>
 <p>In order to classify the HOLE profiles the RMSD to a reference
 structure is calculated for each trajectory frame (e.g. using the
-<a class="reference internal" href="rms.html#MDAnalysis.analysis.rms.RMSD" title="MDAnalysis.analysis.rms.RMSD"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.analysis.rms.RMSD</span></tt></a> analysis class). Then the HOLE
+<a class="reference internal" href="rms.html#MDAnalysis.analysis.rms.RMSD" title="MDAnalysis.analysis.rms.RMSD"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.analysis.rms.RMSD</span></code></a> analysis class). Then the HOLE
 profiles can be ordered by the RMSD, which acts as an order
 parameter.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">MDAnalysis.analysis.hole</span>
@@ -193,10 +193,10 @@ <h3>3.3.1.1.3. Trajectory with RMSD as order parameter<a class="headerlink" href
 <span class="n">H</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
 </pre></div>
 </div>
-<p>The <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj.profiles" title="MDAnalysis.analysis.hole.HOLEtraj.profiles"><tt class="xref py py-attr docutils literal"><span class="pre">HOLEtraj.profiles</span></tt></a> dictionary will have the order parameter as key
+<p>The <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj.profiles" title="MDAnalysis.analysis.hole.HOLEtraj.profiles"><code class="xref py py-attr docutils literal"><span class="pre">HOLEtraj.profiles</span></code></a> dictionary will have the order parameter as key
 for each frame. The plot functions will automatically sort the profiles by
 ascending order parameter. To access the individual profiles one can simply
-iterate over the sorted profiles (see <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj.sorted_profiles_iter" title="MDAnalysis.analysis.hole.HOLEtraj.sorted_profiles_iter"><tt class="xref py py-meth docutils literal"><span class="pre">HOLEtraj.sorted_profiles_iter()</span></tt></a>)</p>
+iterate over the sorted profiles (see <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj.sorted_profiles_iter" title="MDAnalysis.analysis.hole.HOLEtraj.sorted_profiles_iter"><code class="xref py py-meth docutils literal"><span class="pre">HOLEtraj.sorted_profiles_iter()</span></code></a>)</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="k">for</span> <span class="n">q</span><span class="p">,</span> <span class="n">profile</span> <span class="ow">in</span> <span class="n">H</span><span class="p">:</span>
    <span class="k">print</span> <span class="s">&quot;orderparameter = </span><span class="si">%g</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">q</span>
    <span class="k">print</span> <span class="s">&quot;min(R) = </span><span class="si">%g</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">profile</span><span class="o">.</span><span class="n">radius</span><span class="o">.</span><span class="n">min</span><span class="p">()</span>
@@ -206,8 +206,9 @@ <h3>3.3.1.1.3. Trajectory with RMSD as order parameter<a class="headerlink" href
 </div>
 <div class="section" id="data-structures">
 <h2>3.3.1.2. Data structures<a class="headerlink" href="#data-structures" title="Permalink to this headline">¶</a></h2>
-<p>A profile is stored as a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></tt></a>:</p>
-<div class="highlight-python"><pre>frame   rxncoord   radius</pre>
+<p>A profile is stored as a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></code></a>:</p>
+<div class="highlight-python"><div class="highlight"><pre>frame   rxncoord   radius
+</pre></div>
 </div>
 <dl class="docutils">
 <dt>frame</dt>
@@ -218,9 +219,9 @@ <h2>3.3.1.2. Data structures<a class="headerlink" href="#data-structures" title=
 <dt>radius</dt>
 <dd>the pore radius, in Å</dd>
 </dl>
-<p>The <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.profiles" title="MDAnalysis.analysis.hole.HOLE.profiles"><tt class="xref py py-attr docutils literal"><span class="pre">HOLE.profiles</span></tt></a> or <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj.profiles" title="MDAnalysis.analysis.hole.HOLEtraj.profiles"><tt class="xref py py-attr docutils literal"><span class="pre">HOLEtraj.profiles</span></tt></a> dictionary
+<p>The <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.profiles" title="MDAnalysis.analysis.hole.HOLE.profiles"><code class="xref py py-attr docutils literal"><span class="pre">HOLE.profiles</span></code></a> or <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj.profiles" title="MDAnalysis.analysis.hole.HOLEtraj.profiles"><code class="xref py py-attr docutils literal"><span class="pre">HOLEtraj.profiles</span></code></a> dictionary
 holds one profile for each key. By default the keys are the frame
-numbers but <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj" title="MDAnalysis.analysis.hole.HOLEtraj"><tt class="xref py py-class docutils literal"><span class="pre">HOLEtraj</span></tt></a> can take the optional <em>orderparameters</em>
+numbers but <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj" title="MDAnalysis.analysis.hole.HOLEtraj"><code class="xref py py-class docutils literal"><span class="pre">HOLEtraj</span></code></a> can take the optional <em>orderparameters</em>
 keyword argument and load an arbitrary order parameter for each
 frame. In that case, the key becomes the orderparameter.</p>
 <div class="admonition note">
@@ -235,33 +236,34 @@ <h2>3.3.1.2. Data structures<a class="headerlink" href="#data-structures" title=
 <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.analysis.hole.HOLE">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.hole.</tt><tt class="descname">HOLE</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLE"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.hole.</code><code class="descname">HOLE</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLE"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE" title="Permalink to this definition">¶</a></dt>
 <dd><p>Run HOLE on a single frame or a DCD trajectory.</p>
 <p>Only a subset of all <a class="reference external" href="http://s3.smartsci.uk/hole2/doc/old/hole_d03.html">HOLE control parameters</a> is supported and can be set
 with keyword arguments.</p>
 <p>HOLE (as a FORTRAN77 program) has a number of limitations when it comes to
 filename lengths (must be shorter than the empirically found
-<a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.HOLE_MAX_LENGTH" title="MDAnalysis.analysis.hole.HOLE.HOLE_MAX_LENGTH"><tt class="xref py py-attr docutils literal"><span class="pre">HOLE.HOLE_MAX_LENGTH</span></tt></a>). This class tries to work around them by
+<a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.HOLE_MAX_LENGTH" title="MDAnalysis.analysis.hole.HOLE.HOLE_MAX_LENGTH"><code class="xref py py-attr docutils literal"><span class="pre">HOLE.HOLE_MAX_LENGTH</span></code></a>). This class tries to work around them by
 creating temporary symlinks to files when needed but this can still fail
 when permissions are not correctly set on the current directory.</p>
-<p>Running HOLE with the <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE" title="MDAnalysis.analysis.hole.HOLE"><tt class="xref py py-class docutils literal"><span class="pre">HOLE</span></tt></a> class is a 3-step process:</p>
+<p>Running HOLE with the <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE" title="MDAnalysis.analysis.hole.HOLE"><code class="xref py py-class docutils literal"><span class="pre">HOLE</span></code></a> class is a 3-step process:</p>
 <blockquote>
 <div><ol class="arabic simple">
 <li>set up the class with all desired parameters</li>
-<li>run HOLE with <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.run" title="MDAnalysis.analysis.hole.HOLE.run"><tt class="xref py py-meth docutils literal"><span class="pre">HOLE.run()</span></tt></a></li>
-<li>collect the data from the output file with <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.collect" title="MDAnalysis.analysis.hole.HOLE.collect"><tt class="xref py py-meth docutils literal"><span class="pre">HOLE.collect()</span></tt></a></li>
+<li>run HOLE with <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.run" title="MDAnalysis.analysis.hole.HOLE.run"><code class="xref py py-meth docutils literal"><span class="pre">HOLE.run()</span></code></a></li>
+<li>collect the data from the output file with <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.collect" title="MDAnalysis.analysis.hole.HOLE.collect"><code class="xref py py-meth docutils literal"><span class="pre">HOLE.collect()</span></code></a></li>
 </ol>
 </div></blockquote>
 <p>The class also provides some simple plotting functions of the collected
-data such as <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.plot" title="MDAnalysis.analysis.hole.HOLE.plot"><tt class="xref py py-meth docutils literal"><span class="pre">HOLE.plot()</span></tt></a> or <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.plot3D" title="MDAnalysis.analysis.hole.HOLE.plot3D"><tt class="xref py py-meth docutils literal"><span class="pre">HOLE.plot3D()</span></tt></a>.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+data such as <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.plot" title="MDAnalysis.analysis.hole.HOLE.plot"><code class="xref py py-meth docutils literal"><span class="pre">HOLE.plot()</span></code></a> or <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.plot3D" title="MDAnalysis.analysis.hole.HOLE.plot3D"><code class="xref py py-meth docutils literal"><span class="pre">HOLE.plot3D()</span></code></a>.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 <p>Set up parameters to run <a class="reference external" href="http://www.smartsci.uk/hole/">HOLE</a> on PDB <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><p class="first"><em>filename</em></p>
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><p class="first"><em>filename</em></p>
 <blockquote>
 <div><p>The <em>filename</em> is used as input for HOLE in the &#8220;COORD&#8221; card of
 the input file.  It specifies the name of a PDB co-ordinate file
@@ -271,10 +273,10 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 present in the channel these can be ignored on read by the use
 of the <em>ignore_residues</em> keyword.</p>
 <p><strong>Wildcard pattern</strong>. A new feature (in release 2.1 of HOLE) was
-the option to include a wild card (<tt class="docutils literal"><span class="pre">*</span></tt>) in the filename. e.g.,
+the option to include a wild card (<code class="docutils literal"><span class="pre">*</span></code>) in the filename. e.g.,
 <em>filename</em> = <cite>&#8220;ab*.pdb&#8221;</cite> will apply hole to all files in the
-directory whose name starts with <tt class="docutils literal"><span class="pre">ab</span></tt> and ends with
-<tt class="docutils literal"><span class="pre">.pdb</span></tt>. This is intended to aid the analysis of multiple
+directory whose name starts with <code class="docutils literal"><span class="pre">ab</span></code> and ends with
+<code class="docutils literal"><span class="pre">.pdb</span></code>. This is intended to aid the analysis of multiple
 copies of the same molecule - produced during molecular dynamics
 or other method. The hole procedure will be applied to each file
 in turn with the same setup conditions (initial point, sampling
@@ -284,16 +286,16 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 number of atoms or atom order etc. (though they should be
 sufficiently similar for a HOLE run from identical starting
 conditions to be useful).</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">An alternative way to load in multiple files is a direct read
 from a CHARMM binary dynamics DCD coordinate file - using the
-<em>dcd</em> keyword or use <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj" title="MDAnalysis.analysis.hole.HOLEtraj"><tt class="xref py py-class docutils literal"><span class="pre">HOLEtraj</span></tt></a>.</p>
+<em>dcd</em> keyword or use <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj" title="MDAnalysis.analysis.hole.HOLEtraj"><code class="xref py py-class docutils literal"><span class="pre">HOLEtraj</span></code></a>.</p>
 </div>
 </div></blockquote>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>dcd</em></dt>
 <dd><p class="first">DCD trajectory (must be supplied together with a matching
 PDB file <em>filename</em>) and then HOLE runs its analysis on each frame.</p>
@@ -307,14 +309,14 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 format so that it is possible to extract the information from
 the text output file using a <strong class="program">grep</strong> command. The
 reading of the file can be controlled by the <em>step</em> keyword
-and/or setting <tt class="xref py py-attr docutils literal"><span class="pre">HOLE.dcd_iniskip</span></tt> to the number of frames
+and/or setting <code class="xref py py-attr docutils literal"><span class="pre">HOLE.dcd_iniskip</span></code> to the number of frames
 to be skipped initially.</p>
 <div class="last admonition note">
 <p class="first admonition-title">Note</p>
 <p>HOLE is very picky and does not read all DCD-like formats. If
 in doubt, look into the <em>logfile</em> for error diagnostics.</p>
 <p class="last">At the moment, DCDs generated with MDAnalysis are not
-accepted by HOLE — use <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj" title="MDAnalysis.analysis.hole.HOLEtraj"><tt class="xref py py-class docutils literal"><span class="pre">HOLEtraj</span></tt></a>, which works with
+accepted by HOLE — use <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj" title="MDAnalysis.analysis.hole.HOLEtraj"><code class="xref py py-class docutils literal"><span class="pre">HOLEtraj</span></code></a>, which works with
 anything that MDAnalysis can read.</p>
 </div>
 </dd>
@@ -322,7 +324,7 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 <p><em>logfile</em></p>
 <blockquote>
 <div><p>name of the file collecting HOLE&#8217;s output (which can be parsed
-using <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.collect" title="MDAnalysis.analysis.hole.HOLE.collect"><tt class="xref py py-meth docutils literal"><span class="pre">HOLE.collect()</span></tt></a> [&#8220;hole.out&#8221;]</p>
+using <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.collect" title="MDAnalysis.analysis.hole.HOLE.collect"><code class="xref py py-meth docutils literal"><span class="pre">HOLE.collect()</span></code></a> [&#8220;hole.out&#8221;]</p>
 </div></blockquote>
 <p><em>sphpdb</em></p>
 <blockquote>
@@ -336,8 +338,8 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 </div></blockquote>
 <p><em>cpoint</em></p>
 <blockquote>
-<div><p>coordinates of a point inside the pore, e.g. <tt class="docutils literal"><span class="pre">[12.3,</span> <span class="pre">0.7,</span>
-<span class="pre">18.55]</span></tt>. If <tt class="docutils literal"><span class="pre">None</span></tt> then HOLE&#8217;s own simple search algorithm is
+<div><p>coordinates of a point inside the pore, e.g. <code class="docutils literal"><span class="pre">[12.3,</span> <span class="pre">0.7,</span>
+<span class="pre">18.55]</span></code>. If <code class="docutils literal"><span class="pre">None</span></code> then HOLE&#8217;s own simple search algorithm is
 used.</p>
 <p>This specifies a point which lies within the channel, for simple
 channels such as gramicidin results do not show great
@@ -356,19 +358,19 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 grid search up to 5 Å from the original position. This procedure
 works most of the time but is clearly far from infallible —
 results should be careful checked (with molecular graphics) if
-it is used. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+it is used. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </div></blockquote>
 <p><em>cvect</em></p>
 <blockquote>
 <div><p>Search direction, should be parallel to the pore axis,
-e.g. <tt class="docutils literal"><span class="pre">[0,0,1]</span></tt> for the z-axis.</p>
-<p>If this keyword is <tt class="docutils literal"><span class="pre">None</span></tt> then HOLE now attempts to make a
+e.g. <code class="docutils literal"><span class="pre">[0,0,1]</span></code> for the z-axis.</p>
+<p>If this keyword is <code class="docutils literal"><span class="pre">None</span></code> then HOLE now attempts to make a
 guess where the channel will be. The procedure assumes the
 channel is reasonably symmetric. The guess will be either along
 the X axis (1,0,0), Y axis (0,1,0) or Z axis (0,0,1). If the
 structure is not aligned on one of these axis the results will
 clearly be approximate. If a guess is used then results should
-be carefully checked. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+be carefully checked. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </div></blockquote>
 <dl class="docutils">
 <dt><em>sample</em></dt>
@@ -414,12 +416,12 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 <blockquote>
 <div><p>sequence of three-letter residues that are not taken into account during the
 calculation; wildcards are <em>not</em> supported
-[ <tt class="docutils literal"><span class="pre">[&quot;SOL&quot;,&quot;WAT&quot;,</span> <span class="pre">&quot;TIP&quot;,</span> <span class="pre">&quot;HOH&quot;,</span> <span class="pre">&quot;K</span>&nbsp; <span class="pre">&quot;,</span> <span class="pre">&quot;NA</span> <span class="pre">&quot;,</span> <span class="pre">&quot;CL</span> <span class="pre">&quot;]</span></tt> ]</p>
+[ <code class="docutils literal"><span class="pre">[&quot;SOL&quot;,&quot;WAT&quot;,</span> <span class="pre">&quot;TIP&quot;,</span> <span class="pre">&quot;HOH&quot;,</span> <span class="pre">&quot;K</span>&nbsp; <span class="pre">&quot;,</span> <span class="pre">&quot;NA</span> <span class="pre">&quot;,</span> <span class="pre">&quot;CL</span> <span class="pre">&quot;]</span></code> ]</p>
 </div></blockquote>
 <dl class="docutils">
 <dt><em>radius</em></dt>
-<dd><p class="first">Path to the radii; if set to None then a set of default radii, <a class="reference internal" href="#MDAnalysis.analysis.hole.SIMPLE2_RAD" title="MDAnalysis.analysis.hole.SIMPLE2_RAD"><tt class="xref py py-data docutils literal"><span class="pre">SIMPLE2_RAD</span></tt></a>,
-is used (an extension of <tt class="docutils literal"><span class="pre">simple.rad</span></tt> from the HOLE distribution)</p>
+<dd><p class="first">Path to the radii; if set to None then a set of default radii, <a class="reference internal" href="#MDAnalysis.analysis.hole.SIMPLE2_RAD" title="MDAnalysis.analysis.hole.SIMPLE2_RAD"><code class="xref py py-data docutils literal"><span class="pre">SIMPLE2_RAD</span></code></a>,
+is used (an extension of <code class="docutils literal"><span class="pre">simple.rad</span></code> from the HOLE distribution)</p>
 <p class="last">This specifies the name for the file specifying van der Waals
 radii for each atom. A number of files with different values are
 supplied with HOLE.</p>
@@ -447,10 +449,10 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 <p><em>executable</em></p>
 <blockquote class="last">
 <div><p>Path to the <strong class="program">hole</strong> executable
-(e.g. <tt class="docutils literal"><span class="pre">/opt/hole/exe/hole</span></tt>); the other programs
+(e.g. <code class="docutils literal"><span class="pre">/opt/hole/exe/hole</span></code>); the other programs
 <strong class="program">sph_process</strong> and <strong class="program">sos_triangle</strong> are assumed
 to live in the same directory as <strong class="program">hole</strong>. If
-<strong class="program">hole</strong> is found on the <span class="target" id="index-0"></span><a class="reference external" href="http://matplotlib.org/faq/environment_variables_faq.html#envvar-PATH" title="(in Matplotlib v1.4.3)"><tt class="xref std std-envvar docutils literal"><span class="pre">PATH</span></tt></a> then the bare
+<strong class="program">hole</strong> is found on the <span class="target" id="index-0"></span><a class="reference external" href="http://matplotlib.org/faq/environment_variables_faq.html#envvar-PATH" title="(in Matplotlib v1.4.3)"><code class="xref std std-envvar docutils literal"><span class="pre">PATH</span></code></a> then the bare
 executable name is sufficient.  [&#8220;hole&#8221;]</p>
 </div></blockquote>
 </td>
@@ -459,34 +461,34 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 </table>
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.hole.HOLE.profiles">
-<tt class="descname">profiles</tt><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>After running <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.collect" title="MDAnalysis.analysis.hole.HOLE.collect"><tt class="xref py py-meth docutils literal"><span class="pre">HOLE.collect()</span></tt></a>, this dict contains all the
+<code class="descname">profiles</code><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.profiles" title="Permalink to this definition">¶</a></dt>
+<dd><p>After running <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.collect" title="MDAnalysis.analysis.hole.HOLE.collect"><code class="xref py py-meth docutils literal"><span class="pre">HOLE.collect()</span></code></a>, this dict contains all the
 HOLE profiles, indexed by the frame number. If only a single
-frame was analyzed then this will be <tt class="docutils literal"><span class="pre">HOLE.profiles[0]</span></tt>. Note
+frame was analyzed then this will be <code class="docutils literal"><span class="pre">HOLE.profiles[0]</span></code>. Note
 that the order is random; one needs to sort the keys first.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.hole.HOLE.HOLE_MAX_LENGTH">
-<tt class="descname">HOLE_MAX_LENGTH</tt><em class="property"> = 70</em><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.HOLE_MAX_LENGTH" title="Permalink to this definition">¶</a></dt>
+<code class="descname">HOLE_MAX_LENGTH</code><em class="property"> = 70</em><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.HOLE_MAX_LENGTH" title="Permalink to this definition">¶</a></dt>
 <dd><p>Maximum number of characters in a filename (limitation of HOLE)</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLE.check_and_fix_long_filename">
-<tt class="descname">check_and_fix_long_filename</tt><big>(</big><em>filename</em>, <em>tmpdir='.'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLE.check_and_fix_long_filename"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.check_and_fix_long_filename" title="Permalink to this definition">¶</a></dt>
+<code class="descname">check_and_fix_long_filename</code><span class="sig-paren">(</span><em>filename</em>, <em>tmpdir='.'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLE.check_and_fix_long_filename"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.check_and_fix_long_filename" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return <em>filename</em> suitable for HOLE.</p>
-<p>HOLE is limited to filenames &lt;= <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.HOLE_MAX_LENGTH" title="MDAnalysis.analysis.hole.HOLE.HOLE_MAX_LENGTH"><tt class="xref py py-attr docutils literal"><span class="pre">HOLE.HOLE_MAX_LENGTH</span></tt></a>. This method</p>
+<p>HOLE is limited to filenames &lt;= <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.HOLE_MAX_LENGTH" title="MDAnalysis.analysis.hole.HOLE.HOLE_MAX_LENGTH"><code class="xref py py-attr docutils literal"><span class="pre">HOLE.HOLE_MAX_LENGTH</span></code></a>. This method</p>
 <ol class="arabic">
 <li><p class="first">returns <em>filename</em> if HOLE can process it</p>
 </li>
-<li><p class="first">returns a relative path (see <a class="reference external" href="http://docs.python.org/library/os.path.html#os.path.relpath" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">os.path.relpath()</span></tt></a>) if that shortens the
+<li><p class="first">returns a relative path (see <a class="reference external" href="http://docs.python.org/library/os.path.html#os.path.relpath" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">os.path.relpath()</span></code></a>) if that shortens the
 path sufficiently</p>
 </li>
-<li><p class="first">creates a symlink to <em>filename</em> (<a class="reference external" href="http://docs.python.org/library/os.html#os.symlink" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">os.symlink()</span></tt></a>) in a safe temporary
+<li><p class="first">creates a symlink to <em>filename</em> (<a class="reference external" href="http://docs.python.org/library/os.html#os.symlink" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">os.symlink()</span></code></a>) in a safe temporary
 directory and returns the path of the symlink. The temporary directory and
-the symlink are stored in <tt class="xref py py-attr docutils literal"><span class="pre">HOLE.tempfiles</span></tt> and <tt class="xref py py-attr docutils literal"><span class="pre">HOLE.tempdirs</span></tt>
-and deleted when the <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE" title="MDAnalysis.analysis.hole.HOLE"><tt class="xref py py-class docutils literal"><span class="pre">HOLE</span></tt></a> instance is deleted or garbage collected.</p>
+the symlink are stored in <code class="xref py py-attr docutils literal"><span class="pre">HOLE.tempfiles</span></code> and <code class="xref py py-attr docutils literal"><span class="pre">HOLE.tempdirs</span></code>
+and deleted when the <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE" title="MDAnalysis.analysis.hole.HOLE"><code class="xref py py-class docutils literal"><span class="pre">HOLE</span></code></a> instance is deleted or garbage collected.</p>
 <p>By default the temporary directory is created inside the current
 directory in order to keep that path name short. This can be changed
 with the <em>tmpdir</em> keyword (e.g. one can use &#8220;/tmp&#8221;).</p>
@@ -496,27 +498,28 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLE.collect">
-<tt class="descname">collect</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLE.collect"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.collect" title="Permalink to this definition">¶</a></dt>
+<code class="descname">collect</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLE.collect"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.collect" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse the output from a HOLE run into numpy recarrays.</p>
 <p>Can deal with outputs containing multiple frames. Output format:</p>
-<div class="highlight-python"><pre>frame  rxncoord   radius</pre>
+<div class="highlight-python"><div class="highlight"><pre>frame  rxncoord   radius
+</pre></div>
 </div>
-<p>The method saves the result as <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.profiles" title="MDAnalysis.analysis.hole.HOLE.profiles"><tt class="xref py py-attr docutils literal"><span class="pre">HOLE.profiles</span></tt></a>, a dictionary
+<p>The method saves the result as <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.profiles" title="MDAnalysis.analysis.hole.HOLE.profiles"><code class="xref py py-attr docutils literal"><span class="pre">HOLE.profiles</span></code></a>, a dictionary
 indexed by the frame number. Each entry is a
-<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></tt></a>.</p>
+<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.recarray</span></code></a>.</p>
 <p>If the keyword <em>outdir</em> is supplied (e.g. &#8221;.&#8221;) then each profile is
 saved to a gzipped data file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>run</em></dt>
 <dd><p class="first last">identifier, free form [1]</p>
 </dd>
 <dt><em>outdir</em></dt>
 <dd><p class="first last">save output data under <em>outdir</em>/<em>run</em> if set to any other
-value but <tt class="docutils literal"><span class="pre">None</span></tt> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+value but <code class="docutils literal"><span class="pre">None</span></code> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -527,15 +530,16 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLE.create_vmd_surface">
-<tt class="descname">create_vmd_surface</tt><big>(</big><em>filename='hole.vmd'</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLE.create_vmd_surface"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.create_vmd_surface" title="Permalink to this definition">¶</a></dt>
+<code class="descname">create_vmd_surface</code><span class="sig-paren">(</span><em>filename='hole.vmd'</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLE.create_vmd_surface"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.create_vmd_surface" title="Permalink to this definition">¶</a></dt>
 <dd><p>Process HOLE output to create a smooth pore surface suitable for VMD.</p>
-<p>Takes the <tt class="xref py py-attr docutils literal"><span class="pre">sphpdb</span></tt> file and feeds it to <strong class="program">sph_process</strong>
+<p>Takes the <code class="xref py py-attr docutils literal"><span class="pre">sphpdb</span></code> file and feeds it to <strong class="program">sph_process</strong>
 and <strong class="program">sos_triangle</strong> as described under <a class="reference external" href="http://s3.smartsci.uk/hole2/doc/index.html#_producing_a_triangulated_surface_and_visualizing_in_vmd">Visualization of HOLE
 results</a>.</p>
 <p>Load the output file <em>filename</em> into VMD by issuing in the tcl console</p>
-<div class="highlight-python"><pre>source hole.vmd</pre>
+<div class="highlight-python"><div class="highlight"><pre>source hole.vmd
+</pre></div>
 </div>
-<p>The level of detail is determined by <tt class="xref py py-attr docutils literal"><span class="pre">HOLE.dotden</span></tt> (which can be
+<p>The level of detail is determined by <code class="xref py py-attr docutils literal"><span class="pre">HOLE.dotden</span></code> (which can be
 overriden by keyword <em>dotden</em>).</p>
 <p>The surface will be colored so that parts that are inaccessible to
 water (pore radius &lt; 1.15 Å) are red, water accessible parts (1.15 Å &gt;
@@ -545,27 +549,27 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.hole.HOLE.default_ignore_residues">
-<tt class="descname">default_ignore_residues</tt><em class="property"> = ['SOL', 'WAT', 'TIP', 'HOH', 'K  ', 'NA ', 'CL ']</em><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.default_ignore_residues" title="Permalink to this definition">¶</a></dt>
+<code class="descname">default_ignore_residues</code><em class="property"> = ['SOL', 'WAT', 'TIP', 'HOH', 'K  ', 'NA ', 'CL ']</em><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.default_ignore_residues" title="Permalink to this definition">¶</a></dt>
 <dd><p>List of residues that are ignore by default. Can be changed with
 the <em>ignore_residues</em> keyword.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLE.min_radius">
-<tt class="descname">min_radius</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.min_radius" title="Permalink to this definition">¶</a></dt>
+<code class="descname">min_radius</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.min_radius" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return the minimum radius over all profiles as a function of q</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLE.plot">
-<tt class="descname">plot</tt><big>(</big><em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.plot" title="Permalink to this definition">¶</a></dt>
+<code class="descname">plot</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.plot" title="Permalink to this definition">¶</a></dt>
 <dd><p>Plot profiles in a 1D graph.</p>
 <p>Lines are coloured according to the colour map <em>cmap</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>step</em></dt>
 <dd><p class="first last">only plot every <em>step</em> profile [1]</p>
 </dd>
@@ -574,10 +578,10 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 </dd>
 <dt><em>color</em></dt>
 <dd><p class="first last">color or iterable of colors to specify graph colors;
-<tt class="docutils literal"><span class="pre">None</span></tt> will use <em>cmap</em> instead [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<code class="docutils literal"><span class="pre">None</span></code> will use <em>cmap</em> instead [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>linestyle</em></dt>
-<dd><p class="first last">linestyle supported by <a class="reference external" href="http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.plot" title="(in Matplotlib v1.4.3)"><tt class="xref py py-func docutils literal"><span class="pre">matplotlib.pyplot.plot()</span></tt></a>;
+<dd><p class="first last">linestyle supported by <a class="reference external" href="http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.plot" title="(in Matplotlib v1.4.3)"><code class="xref py py-func docutils literal"><span class="pre">matplotlib.pyplot.plot()</span></code></a>;
 an iterable will be applied in turn [&#8216;-&#8216;]</p>
 </dd>
 <dt><em>yshift</em></dt>
@@ -587,35 +591,35 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 <dt><em>frames</em></dt>
 <dd><p class="first last">integer or list: only plot these specific frame(s);
 the default is to plot everything (see also <em>step</em>).
-[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+[<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>label</em></dt>
 <dd><p class="first last">ignored and replaced with the frame number; if it
-is set to &#8220;_nolegend_&#8221; or <tt class="docutils literal"><span class="pre">False</span></tt> then no
+is set to &#8220;_nolegend_&#8221; or <code class="docutils literal"><span class="pre">False</span></code> then no
 legend is displayed</p>
 </dd>
 <dt><em>ax</em></dt>
-<dd><p class="first last"><a class="reference external" href="http://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes" title="(in Matplotlib v1.4.3)"><tt class="xref py py-class docutils literal"><span class="pre">matplotlib.axes.Axes</span></tt></a> instance to plot into
-[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last"><a class="reference external" href="http://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes" title="(in Matplotlib v1.4.3)"><code class="xref py py-class docutils literal"><span class="pre">matplotlib.axes.Axes</span></code></a> instance to plot into
+[<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p>All other <em>kwargs</em> are passed to <a class="reference external" href="http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.plot" title="(in Matplotlib v1.4.3)"><tt class="xref py py-func docutils literal"><span class="pre">matplotlib.pyplot.plot()</span></tt></a>.</p>
+<p>All other <em>kwargs</em> are passed to <a class="reference external" href="http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.plot" title="(in Matplotlib v1.4.3)"><code class="xref py py-func docutils literal"><span class="pre">matplotlib.pyplot.plot()</span></code></a>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLE.plot3D">
-<tt class="descname">plot3D</tt><big>(</big><em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.plot3D" title="Permalink to this definition">¶</a></dt>
+<code class="descname">plot3D</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.plot3D" title="Permalink to this definition">¶</a></dt>
 <dd><p>Stacked graph of profiles.</p>
 <p>Lines are coloured according to the colour map <em>cmap</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>step</em></dt>
 <dd><p class="first last">only plot every <em>step</em> profile [1]</p>
 </dd>
@@ -623,7 +627,7 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 <dd><p class="first last">matplotlib color map [jet]</p>
 </dd>
 <dt><em>rmax</em></dt>
-<dd><p class="first last">only display radii up to <em>rmax</em> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">only display radii up to <em>rmax</em> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>ylabel</em></dt>
 <dd><p class="first last">label of the reaction coordinate axis [&#8220;frames&#8221;]</p>
@@ -638,14 +642,14 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLE.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLE.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLE.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Run HOLE on the input file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLE.save">
-<tt class="descname">save</tt><big>(</big><em>filename='hole.pickle'</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.save" title="Permalink to this definition">¶</a></dt>
-<dd><p>Save <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.profiles" title="MDAnalysis.analysis.hole.HOLE.profiles"><tt class="xref py py-attr docutils literal"><span class="pre">profiles</span></tt></a> as a Python pickle file <em>filename</em>.</p>
+<code class="descname">save</code><span class="sig-paren">(</span><em>filename='hole.pickle'</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.save" title="Permalink to this definition">¶</a></dt>
+<dd><p>Save <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.profiles" title="MDAnalysis.analysis.hole.HOLE.profiles"><code class="xref py py-attr docutils literal"><span class="pre">profiles</span></code></a> as a Python pickle file <em>filename</em>.</p>
 <p>Load profiles dictionary with</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">cPickle</span>
 <span class="n">profiles</span> <span class="o">=</span> <span class="n">cPickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
@@ -655,18 +659,18 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLE.sorted_profiles_iter">
-<tt class="descname">sorted_profiles_iter</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.sorted_profiles_iter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sorted_profiles_iter</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLE.sorted_profiles_iter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return an iterator over profiles sorted by frame/order parameter <em>q</em>.</p>
-<p>The iterator produces tuples <tt class="docutils literal"><span class="pre">(q,</span> <span class="pre">profile)</span></tt>.</p>
+<p>The iterator produces tuples <code class="docutils literal"><span class="pre">(q,</span> <span class="pre">profile)</span></code>.</p>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.hole.HOLEtraj">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.hole.</tt><tt class="descname">HOLEtraj</tt><big>(</big><em>universe</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLEtraj"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.hole.</code><code class="descname">HOLEtraj</code><span class="sig-paren">(</span><em>universe</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLEtraj"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj" title="Permalink to this definition">¶</a></dt>
 <dd><p>Analyze all frames in a trajectory.</p>
-<p>The <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE" title="MDAnalysis.analysis.hole.HOLE"><tt class="xref py py-class docutils literal"><span class="pre">HOLE</span></tt></a> class provides a direct interface to HOLE. HOLE itself
+<p>The <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE" title="MDAnalysis.analysis.hole.HOLE"><code class="xref py py-class docutils literal"><span class="pre">HOLE</span></code></a> class provides a direct interface to HOLE. HOLE itself
 has limited support for analysing trajectories but cannot deal with all the
 trajectory formats understood by MDAnalysis. This class can take any
 universe and feed it to HOLE. By default it sequentially creates a PDB for
@@ -676,10 +680,10 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">The input trajectory as part of a
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>. trajectory is
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>. trajectory is
 converted to a sequence of PDB files and HOLE is run on each
 individual file. (Use the <em>start</em>, <em>stop</em>, and <em>step</em> keywords
 to slice the trajectory.)</p>
@@ -690,22 +694,22 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 </dd>
 <dt><em>start</em>, <em>stop</em>, <em>step</em></dt>
 <dd><p class="first last">frame indices to slice the trajectory as
-<tt class="docutils literal"><span class="pre">universe.trajectory[start,</span> <span class="pre">stop,</span> <span class="pre">step]</span></tt></p>
+<code class="docutils literal"><span class="pre">universe.trajectory[start,</span> <span class="pre">stop,</span> <span class="pre">step]</span></code></p>
 </dd>
 <dt><em>selection</em></dt>
-<dd><p class="first last">selection string for <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> to select
+<dd><p class="first last">selection string for <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> to select
 the group of atoms that is to be analysed by HOLE [&#8220;protein&#8221;]</p>
 </dd>
 <dt><em>cpoint</em></dt>
 <dd><p class="first">Point inside the pore.</p>
-<p>If set to <tt class="docutils literal"><span class="pre">True</span></tt> then <em>cpoint</em> is guessed as the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry" title="MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry"><tt class="xref py py-meth docutils literal"><span class="pre">centerOfGeometry()</span></tt></a> of
+<p>If set to <code class="docutils literal"><span class="pre">True</span></code> then <em>cpoint</em> is guessed as the
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry" title="MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry"><code class="xref py py-meth docutils literal"><span class="pre">center_of_geometry()</span></code></a> of
 the <em>selection</em> from the first frame of the trajectory.</p>
-<p class="last">If <em>cpoint</em> is not set or set to <tt class="docutils literal"><span class="pre">None</span></tt> then HOLE guesses it
-with its own algorithm (for each individual frame). [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<p class="last">If <em>cpoint</em> is not set or set to <code class="docutils literal"><span class="pre">None</span></code> then HOLE guesses it
+with its own algorithm (for each individual frame). [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>kwargs</em></dt>
-<dd><p class="first last">All other keywords are passed on to <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE" title="MDAnalysis.analysis.hole.HOLE"><tt class="xref py py-class docutils literal"><span class="pre">HOLE</span></tt></a> (see there for description).</p>
+<dd><p class="first last">All other keywords are passed on to <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE" title="MDAnalysis.analysis.hole.HOLE"><code class="xref py py-class docutils literal"><span class="pre">HOLE</span></code></a> (see there for description).</p>
 </dd>
 </dl>
 </td>
@@ -714,8 +718,8 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 </table>
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.hole.HOLEtraj.profiles">
-<tt class="descname">profiles</tt><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>After running <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.collect" title="MDAnalysis.analysis.hole.HOLE.collect"><tt class="xref py py-meth docutils literal"><span class="pre">HOLE.collect()</span></tt></a>, this dict contains all the
+<code class="descname">profiles</code><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.profiles" title="Permalink to this definition">¶</a></dt>
+<dd><p>After running <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLE.collect" title="MDAnalysis.analysis.hole.HOLE.collect"><code class="xref py py-meth docutils literal"><span class="pre">HOLE.collect()</span></code></a>, this dict contains all the
 HOLE profiles, indexed by the frame number or the order
 parameter (if <em>orderparameters</em> was supplied). Note that the
 order is random; one needs to sort the keys first.</p>
@@ -723,7 +727,7 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLEtraj.guess_cpoint">
-<tt class="descname">guess_cpoint</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLEtraj.guess_cpoint"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.guess_cpoint" title="Permalink to this definition">¶</a></dt>
+<code class="descname">guess_cpoint</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLEtraj.guess_cpoint"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.guess_cpoint" title="Permalink to this definition">¶</a></dt>
 <dd><p>Guess a point inside the pore.</p>
 <p>This method simply uses the center of geometry of the protein selection
 as a guess. <em>selection</em> is &#8220;protein&#8221; by default.</p>
@@ -731,20 +735,20 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLEtraj.min_radius">
-<tt class="descname">min_radius</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.min_radius" title="Permalink to this definition">¶</a></dt>
+<code class="descname">min_radius</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.min_radius" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return the minimum radius over all profiles as a function of q</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLEtraj.plot">
-<tt class="descname">plot</tt><big>(</big><em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.plot" title="Permalink to this definition">¶</a></dt>
+<code class="descname">plot</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.plot" title="Permalink to this definition">¶</a></dt>
 <dd><p>Plot profiles in a 1D graph.</p>
 <p>Lines are coloured according to the colour map <em>cmap</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>step</em></dt>
 <dd><p class="first last">only plot every <em>step</em> profile [1]</p>
 </dd>
@@ -753,10 +757,10 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 </dd>
 <dt><em>color</em></dt>
 <dd><p class="first last">color or iterable of colors to specify graph colors;
-<tt class="docutils literal"><span class="pre">None</span></tt> will use <em>cmap</em> instead [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<code class="docutils literal"><span class="pre">None</span></code> will use <em>cmap</em> instead [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>linestyle</em></dt>
-<dd><p class="first last">linestyle supported by <a class="reference external" href="http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.plot" title="(in Matplotlib v1.4.3)"><tt class="xref py py-func docutils literal"><span class="pre">matplotlib.pyplot.plot()</span></tt></a>;
+<dd><p class="first last">linestyle supported by <a class="reference external" href="http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.plot" title="(in Matplotlib v1.4.3)"><code class="xref py py-func docutils literal"><span class="pre">matplotlib.pyplot.plot()</span></code></a>;
 an iterable will be applied in turn [&#8216;-&#8216;]</p>
 </dd>
 <dt><em>yshift</em></dt>
@@ -766,35 +770,35 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 <dt><em>frames</em></dt>
 <dd><p class="first last">integer or list: only plot these specific frame(s);
 the default is to plot everything (see also <em>step</em>).
-[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+[<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>label</em></dt>
 <dd><p class="first last">ignored and replaced with the frame number; if it
-is set to &#8220;_nolegend_&#8221; or <tt class="docutils literal"><span class="pre">False</span></tt> then no
+is set to &#8220;_nolegend_&#8221; or <code class="docutils literal"><span class="pre">False</span></code> then no
 legend is displayed</p>
 </dd>
 <dt><em>ax</em></dt>
-<dd><p class="first last"><a class="reference external" href="http://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes" title="(in Matplotlib v1.4.3)"><tt class="xref py py-class docutils literal"><span class="pre">matplotlib.axes.Axes</span></tt></a> instance to plot into
-[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last"><a class="reference external" href="http://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes" title="(in Matplotlib v1.4.3)"><code class="xref py py-class docutils literal"><span class="pre">matplotlib.axes.Axes</span></code></a> instance to plot into
+[<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p>All other <em>kwargs</em> are passed to <a class="reference external" href="http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.plot" title="(in Matplotlib v1.4.3)"><tt class="xref py py-func docutils literal"><span class="pre">matplotlib.pyplot.plot()</span></tt></a>.</p>
+<p>All other <em>kwargs</em> are passed to <a class="reference external" href="http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.plot" title="(in Matplotlib v1.4.3)"><code class="xref py py-func docutils literal"><span class="pre">matplotlib.pyplot.plot()</span></code></a>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLEtraj.plot3D">
-<tt class="descname">plot3D</tt><big>(</big><em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.plot3D" title="Permalink to this definition">¶</a></dt>
+<code class="descname">plot3D</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.plot3D" title="Permalink to this definition">¶</a></dt>
 <dd><p>Stacked graph of profiles.</p>
 <p>Lines are coloured according to the colour map <em>cmap</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>step</em></dt>
 <dd><p class="first last">only plot every <em>step</em> profile [1]</p>
 </dd>
@@ -802,7 +806,7 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 <dd><p class="first last">matplotlib color map [jet]</p>
 </dd>
 <dt><em>rmax</em></dt>
-<dd><p class="first last">only display radii up to <em>rmax</em> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">only display radii up to <em>rmax</em> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>ylabel</em></dt>
 <dd><p class="first last">label of the reaction coordinate axis [&#8220;frames&#8221;]</p>
@@ -817,7 +821,7 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLEtraj.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLEtraj.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLEtraj.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Run HOLE on the whole trajectory and collect profiles.</p>
 <p>Keyword arguments <em>start</em>, <em>stop</em>, and <em>step</em> can be used to only
 analyse part of the trajectory.</p>
@@ -825,14 +829,14 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLEtraj.run_hole">
-<tt class="descname">run_hole</tt><big>(</big><em>pdbfile</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLEtraj.run_hole"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.run_hole" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run_hole</code><span class="sig-paren">(</span><em>pdbfile</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#HOLEtraj.run_hole"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.run_hole" title="Permalink to this definition">¶</a></dt>
 <dd><p>Run HOLE on a single PDB file <em>pdbfile</em>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLEtraj.save">
-<tt class="descname">save</tt><big>(</big><em>filename='hole.pickle'</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.save" title="Permalink to this definition">¶</a></dt>
-<dd><p>Save <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj.profiles" title="MDAnalysis.analysis.hole.HOLEtraj.profiles"><tt class="xref py py-attr docutils literal"><span class="pre">profiles</span></tt></a> as a Python pickle file <em>filename</em>.</p>
+<code class="descname">save</code><span class="sig-paren">(</span><em>filename='hole.pickle'</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.save" title="Permalink to this definition">¶</a></dt>
+<dd><p>Save <a class="reference internal" href="#MDAnalysis.analysis.hole.HOLEtraj.profiles" title="MDAnalysis.analysis.hole.HOLEtraj.profiles"><code class="xref py py-attr docutils literal"><span class="pre">profiles</span></code></a> as a Python pickle file <em>filename</em>.</p>
 <p>Load profiles dictionary with</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">cPickle</span>
 <span class="n">profiles</span> <span class="o">=</span> <span class="n">cPickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
@@ -842,21 +846,21 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.hole.HOLEtraj.sorted_profiles_iter">
-<tt class="descname">sorted_profiles_iter</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.sorted_profiles_iter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sorted_profiles_iter</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.hole.HOLEtraj.sorted_profiles_iter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return an iterator over profiles sorted by frame/order parameter <em>q</em>.</p>
-<p>The iterator produces tuples <tt class="docutils literal"><span class="pre">(q,</span> <span class="pre">profile)</span></tt>.</p>
+<p>The iterator produces tuples <code class="docutils literal"><span class="pre">(q,</span> <span class="pre">profile)</span></code>.</p>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.analysis.hole.SIMPLE2_RAD">
-<tt class="descclassname">MDAnalysis.analysis.hole.</tt><tt class="descname">SIMPLE2_RAD</tt><em class="property"> = '\nremark: Time-stamp: &lt;2005-11-21 13:57:55 oliver&gt; [OB]\nremark: van der Waals radii: AMBER united atom\nremark: from Weiner et al. (1984), JACS, vol 106 pp765-768\nremark: Simple - Only use one value for each element C O H etc.\nremark: van der Waals radii\nremark: general last\nVDWR C??? ??? 1.85\nVDWR O??? ??? 1.65\nVDWR S??? ??? 2.00\nVDWR N??? ??? 1.75\nVDWR H??? ??? 1.00\nVDWR H?   ??? 1.00\nVDWR P??? ??? 2.10\nremark: ASN, GLN polar H (odd names for these atoms in xplor)\nVDWR E2?  GLN 1.00\nVDWR D2?  ASN 1.00\nremark: amber lone pairs on sulphurs\nVDWR LP?? ??? 0.00\nremark: for some funny reason it wants radius for K even though\nremark: it is on the exclude list\nremark: Use Pauling hydration radius (Hille 2001) [OB]\nVDWR K?   ??? 1.33\nVDWR NA?  ??? 0.95\nVDWR CL?  ??? 1.81\nremark: funny hydrogens in gA structure [OB]\nVDWR 1H?  ??? 1.00\nVDWR 2H?  ??? 1.00\nVDWR 3H?  ??? 1.00\nremark: need bond rad for molqpt option\nBOND C??? 0.85\nBOND N??? 0.75\nBOND O??? 0.7\nBOND S??? 1.1\nBOND H??? 0.5\nBOND P??? 1.0\nBOND ???? 0.85\n'</em><a class="headerlink" href="#MDAnalysis.analysis.hole.SIMPLE2_RAD" title="Permalink to this definition">¶</a></dt>
-<dd><p>Built-in HOLE radii (based on <tt class="docutils literal"><span class="pre">simple.rad</span></tt> from the <a class="reference external" href="http://www.smartsci.uk/hole/">HOLE</a> distribution):
+<code class="descclassname">MDAnalysis.analysis.hole.</code><code class="descname">SIMPLE2_RAD</code><em class="property"> = '\nremark: Time-stamp: &lt;2005-11-21 13:57:55 oliver&gt; [OB]\nremark: van der Waals radii: AMBER united atom\nremark: from Weiner et al. (1984), JACS, vol 106 pp765-768\nremark: Simple - Only use one value for each element C O H etc.\nremark: van der Waals radii\nremark: general last\nVDWR C??? ??? 1.85\nVDWR O??? ??? 1.65\nVDWR S??? ??? 2.00\nVDWR N??? ??? 1.75\nVDWR H??? ??? 1.00\nVDWR H?   ??? 1.00\nVDWR P??? ??? 2.10\nremark: ASN, GLN polar H (odd names for these atoms in xplor)\nVDWR E2?  GLN 1.00\nVDWR D2?  ASN 1.00\nremark: amber lone pairs on sulphurs\nVDWR LP?? ??? 0.00\nremark: for some funny reason it wants radius for K even though\nremark: it is on the exclude list\nremark: Use Pauling hydration radius (Hille 2001) [OB]\nVDWR K?   ??? 1.33\nVDWR NA?  ??? 0.95\nVDWR CL?  ??? 1.81\nremark: funny hydrogens in gA structure [OB]\nVDWR 1H?  ??? 1.00\nVDWR 2H?  ??? 1.00\nVDWR 3H?  ??? 1.00\nremark: need bond rad for molqpt option\nBOND C??? 0.85\nBOND N??? 0.75\nBOND O??? 0.7\nBOND S??? 1.1\nBOND H??? 0.5\nBOND P??? 1.0\nBOND ???? 0.85\n'</em><a class="headerlink" href="#MDAnalysis.analysis.hole.SIMPLE2_RAD" title="Permalink to this definition">¶</a></dt>
+<dd><p>Built-in HOLE radii (based on <code class="docutils literal"><span class="pre">simple.rad</span></code> from the <a class="reference external" href="http://www.smartsci.uk/hole/">HOLE</a> distribution):
 van der Waals radii are AMBER united atom from Weiner et al. (1984), JACS, vol 106 pp765-768.
 <em>Simple</em> - Only use one value for each element C O H etc.
 Added radii for K+, NA+, CL- (Pauling hydration radius from Hille 2002).
-The data file can be written with the convenience function <a class="reference internal" href="#MDAnalysis.analysis.hole.write_simplerad2" title="MDAnalysis.analysis.hole.write_simplerad2"><tt class="xref py py-func docutils literal"><span class="pre">write_simplerad2()</span></tt></a>.</p>
+The data file can be written with the convenience function <a class="reference internal" href="#MDAnalysis.analysis.hole.write_simplerad2" title="MDAnalysis.analysis.hole.write_simplerad2"><code class="xref py py-func docutils literal"><span class="pre">write_simplerad2()</span></code></a>.</p>
 </dd></dl>
 
 </div>
@@ -864,25 +868,26 @@ <h2>3.3.1.3. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 <h2>3.3.1.4. Utilities<a class="headerlink" href="#utilities" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.analysis.hole.write_simplerad2">
-<tt class="descclassname">MDAnalysis.analysis.hole.</tt><tt class="descname">write_simplerad2</tt><big>(</big><em>filename='simple2.rad'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#write_simplerad2"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.write_simplerad2" title="Permalink to this definition">¶</a></dt>
-<dd><p>Write the built-in radii in <a class="reference internal" href="#MDAnalysis.analysis.hole.SIMPLE2_RAD" title="MDAnalysis.analysis.hole.SIMPLE2_RAD"><tt class="xref py py-data docutils literal"><span class="pre">SIMPLE2_RAD</span></tt></a> to <em>filename</em>.</p>
+<code class="descclassname">MDAnalysis.analysis.hole.</code><code class="descname">write_simplerad2</code><span class="sig-paren">(</span><em>filename='simple2.rad'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#write_simplerad2"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.write_simplerad2" title="Permalink to this definition">¶</a></dt>
+<dd><p>Write the built-in radii in <a class="reference internal" href="#MDAnalysis.analysis.hole.SIMPLE2_RAD" title="MDAnalysis.analysis.hole.SIMPLE2_RAD"><code class="xref py py-data docutils literal"><span class="pre">SIMPLE2_RAD</span></code></a> to <em>filename</em>.</p>
 <p>Does nothing if <em>filename</em> already exists.</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.hole.seq2str">
-<tt class="descclassname">MDAnalysis.analysis.hole.</tt><tt class="descname">seq2str</tt><big>(</big><em>v</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#seq2str"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.seq2str" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.hole.</code><code class="descname">seq2str</code><span class="sig-paren">(</span><em>v</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/hole.html#seq2str"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.seq2str" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return sequence <em>v</em> as a string of numbers with spaces as separators.</p>
-<p>In the special case of <tt class="docutils literal"><span class="pre">None</span></tt>, the empty string &#8220;&#8221; is returned.</p>
+<p>In the special case of <code class="docutils literal"><span class="pre">None</span></code>, the empty string &#8220;&#8221; is returned.</p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.hole.ApplicationError">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.hole.</tt><tt class="descname">ApplicationError</tt><a class="headerlink" href="#MDAnalysis.analysis.hole.ApplicationError" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.hole.</code><code class="descname">ApplicationError</code><a class="reference internal" href="../../_modules/MDAnalysis/exceptions.html#ApplicationError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.hole.ApplicationError" title="Permalink to this definition">¶</a></dt>
 <dd><p>Raised when an external application failed.</p>
 <p>The error code is specific for the application.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 </div>
@@ -894,7 +899,7 @@ <h2>3.3.1.4. Utilities<a class="headerlink" href="#utilities" title="Permalink t
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -909,11 +914,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="hbond_autocorrel.html" title="3.2.2. Hydrogen bond autocorrelation — MDAnalysis.analysis.hbonds.hbond_autocorrel"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -923,7 +928,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/leaflet.html b/package/doc/html/documentation_pages/analysis/leaflet.html
index 3213ef4593d..3e1d8ae03c0 100644
--- a/package/doc/html/documentation_pages/analysis/leaflet.html
+++ b/package/doc/html/documentation_pages/analysis/leaflet.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.3.2. Leaflet identification — MDAnalysis.analysis.leaflet &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.3.2. Leaflet identification — MDAnalysis.analysis.leaflet &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="3.4.1. Nucleic acid analysis — MDAnalysis.analysis.nuclinfo" href="nuclinfo.html" />
     <link rel="prev" title="3.3.1. Generation and Analysis of HOLE pore profiles — MDAnalysis.analysis.hole" href="hole.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="hole.html" title="3.3.1. Generation and Analysis of HOLE pore profiles — MDAnalysis.analysis.hole"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="hole.html"
-                        title="previous chapter">3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.analysis.hole</span></tt></a></p>
+                        title="previous chapter">3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.hole</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="nuclinfo.html"
-                        title="next chapter">3.4.1. Nucleic acid analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.nuclinfo</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/analysis/leaflet.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">3.4.1. Nucleic acid analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.nuclinfo</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/analysis/leaflet.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,10 +90,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.leaflet"></span><div class="section" id="leaflet-identification-mdanalysis-analysis-leaflet">
-<h1>3.3.2. Leaflet identification &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.leaflet" title="MDAnalysis.analysis.leaflet"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.leaflet</span></tt></a><a class="headerlink" href="#leaflet-identification-mdanalysis-analysis-leaflet" title="Permalink to this headline">¶</a></h1>
+<h1>3.3.2. Leaflet identification &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.leaflet" title="MDAnalysis.analysis.leaflet"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.leaflet</span></code></a><a class="headerlink" href="#leaflet-identification-mdanalysis-analysis-leaflet" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -118,24 +118,24 @@ <h1>3.3.2. Leaflet identification &#8212; <a class="reference internal" href="#m
 <p>One can use this information to identify</p>
 <ul class="simple">
 <li>the upper and lower leaflet of a <em>planar membrane</em> by comparing the
-the <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry" title="MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry"><tt class="xref py py-meth docutils literal"><span class="pre">centerOfGeometry()</span></tt></a> of
+the <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry" title="MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry"><code class="xref py py-meth docutils literal"><span class="pre">center_of_geometry()</span></code></a> of
 the leaflet groups, or</li>
 <li>the outer and inner leaflet of a <em>vesicle</em> by comparing histograms
 of distances from the centre of geometry (or possibly simply the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.radiusOfGyration" title="MDAnalysis.core.AtomGroup.AtomGroup.radiusOfGyration"><tt class="xref py py-meth docutils literal"><span class="pre">radiusOfGyration()</span></tt></a>).</li>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.radius_of_gyration" title="MDAnalysis.core.AtomGroup.AtomGroup.radius_of_gyration"><code class="xref py py-meth docutils literal"><span class="pre">radius_of_gyration()</span></code></a>).</li>
 </ul>
-<p>See example scripts in the <tt class="docutils literal"><span class="pre">examples/</span></tt> directory on how to use
-<a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder" title="MDAnalysis.analysis.leaflet.LeafletFinder"><tt class="xref py py-class docutils literal"><span class="pre">LeafletFinder</span></tt></a>. The function <a class="reference internal" href="#MDAnalysis.analysis.leaflet.optimize_cutoff" title="MDAnalysis.analysis.leaflet.optimize_cutoff"><tt class="xref py py-func docutils literal"><span class="pre">optimize_cutoff()</span></tt></a> implements a
+<p>See example scripts in the <code class="docutils literal"><span class="pre">examples/</span></code> directory on how to use
+<a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder" title="MDAnalysis.analysis.leaflet.LeafletFinder"><code class="xref py py-class docutils literal"><span class="pre">LeafletFinder</span></code></a>. The function <a class="reference internal" href="#MDAnalysis.analysis.leaflet.optimize_cutoff" title="MDAnalysis.analysis.leaflet.optimize_cutoff"><code class="xref py py-func docutils literal"><span class="pre">optimize_cutoff()</span></code></a> implements a
 (slow) heuristic method to find the best cut off for the LeafletFinder
 algorithm.</p>
 <dl class="class">
 <dt id="MDAnalysis.analysis.leaflet.LeafletFinder">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.leaflet.</tt><tt class="descname">LeafletFinder</tt><big>(</big><em>universe</em>, <em>selectionstring</em>, <em>cutoff=15.0</em>, <em>pbc=False</em>, <em>sparse=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.leaflet.</code><code class="descname">LeafletFinder</code><span class="sig-paren">(</span><em>universe</em>, <em>selectionstring</em>, <em>cutoff=15.0</em>, <em>pbc=False</em>, <em>sparse=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder" title="Permalink to this definition">¶</a></dt>
 <dd><p>Identify atoms in the same leaflet of a lipid bilayer.</p>
 <p>The components of the graph are stored in the list
-<tt class="xref py py-attr docutils literal"><span class="pre">LeafletFinder.components</span></tt>; the atoms in each component are numbered
+<code class="xref py py-attr docutils literal"><span class="pre">LeafletFinder.components</span></code>; the atoms in each component are numbered
 consecutively, starting at 0. To obtain the atoms in the input structure
-use <a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder.groups" title="MDAnalysis.analysis.leaflet.LeafletFinder.groups"><tt class="xref py py-meth docutils literal"><span class="pre">LeafletFinder.groups()</span></tt></a>:</p>
+use <a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder.groups" title="MDAnalysis.analysis.leaflet.LeafletFinder.groups"><code class="xref py py-meth docutils literal"><span class="pre">LeafletFinder.groups()</span></code></a>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">L</span> <span class="o">=</span> <span class="n">LeafletFinder</span><span class="p">(</span><span class="n">PDB</span><span class="p">,</span> <span class="s">&#39;name P*&#39;</span><span class="p">)</span>
 <span class="n">leaflet0</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
 <span class="n">leaflet1</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
@@ -145,7 +145,7 @@ <h1>3.3.2. Leaflet identification &#8212; <a class="reference internal" href="#m
 <div class="highlight-python"><div class="highlight"><pre><span class="n">leaflet0</span><span class="o">.</span><span class="n">residues</span>
 </pre></div>
 </div>
-<p>provides a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a>
+<p>provides a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>
 instance. Similarly, all atoms in the first leaflet are then</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">leaflet0</span><span class="o">.</span><span class="n">residues</span><span class="o">.</span><span class="n">atoms</span>
 </pre></div>
@@ -155,33 +155,33 @@ <h1>3.3.2. Leaflet identification &#8212; <a class="reference internal" href="#m
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> or a PDB file name.</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> or a PDB file name.</p>
 </dd>
 <dt><em>selection</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> or a
-<tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.Universe.select_atoms()</span></tt> selection string
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> or a
+<code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.Universe.select_atoms()</span></code> selection string
 for atoms that define the lipid head groups, e.g.
 universe.atoms.PO4 or &#8220;name PO4&#8221; or &#8220;name P*&#8221;</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>cutoff</em></dt>
 <dd><p class="first last">head group-defining atoms within a distance of <em>cutoff</em>
 Angstroms are deemed to be in the same leaflet [15.0]</p>
 </dd>
 <dt><em>pbc</em></dt>
 <dd><p class="first last">take periodic boundary conditions into account (only works
-for orthorhombic boxes) [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+for orthorhombic boxes) [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>sparse</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">None</span></tt>: use fastest possible routine; <tt class="docutils literal"><span class="pre">True</span></tt>: use slow
-sparse matrix implementation (for large systems); <tt class="docutils literal"><span class="pre">False</span></tt>:
-use fast <a class="reference internal" href="distances.html#MDAnalysis.analysis.distances.distance_array" title="MDAnalysis.analysis.distances.distance_array"><tt class="xref py py-func docutils literal"><span class="pre">distance_array()</span></tt></a>
-implementation [<tt class="docutils literal"><span class="pre">None</span></tt>].</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">None</span></code>: use fastest possible routine; <code class="docutils literal"><span class="pre">True</span></code>: use slow
+sparse matrix implementation (for large systems); <code class="docutils literal"><span class="pre">False</span></code>:
+use fast <a class="reference internal" href="distances.html#MDAnalysis.analysis.distances.distance_array" title="MDAnalysis.analysis.distances.distance_array"><code class="xref py py-func docutils literal"><span class="pre">distance_array()</span></code></a>
+implementation [<code class="docutils literal"><span class="pre">None</span></code>].</p>
 </dd>
 </dl>
 </td>
@@ -190,46 +190,46 @@ <h1>3.3.2. Leaflet identification &#8212; <a class="reference internal" href="#m
 </table>
 <dl class="method">
 <dt id="MDAnalysis.analysis.leaflet.LeafletFinder.group">
-<tt class="descname">group</tt><big>(</big><em>component_index</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.group"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.group" title="Permalink to this definition">¶</a></dt>
-<dd><p>Return a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> for <em>component_index</em>.</p>
+<code class="descname">group</code><span class="sig-paren">(</span><em>component_index</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.group"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.group" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> for <em>component_index</em>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.leaflet.LeafletFinder.groups">
-<tt class="descname">groups</tt><big>(</big><em>component_index=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.groups"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.groups" title="Permalink to this definition">¶</a></dt>
-<dd><p>Return a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> for <em>component_index</em>.</p>
+<code class="descname">groups</code><span class="sig-paren">(</span><em>component_index=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.groups"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.groups" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> for <em>component_index</em>.</p>
 <p>If no argument is supplied, then a list of all leaflet groups is returned.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder.group" title="MDAnalysis.analysis.leaflet.LeafletFinder.group"><tt class="xref py py-meth docutils literal"><span class="pre">LeafletFinder.group()</span></tt></a> and <a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter" title="MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter"><tt class="xref py py-meth docutils literal"><span class="pre">LeafletFinder.groups_iter()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder.group" title="MDAnalysis.analysis.leaflet.LeafletFinder.group"><code class="xref py py-meth docutils literal"><span class="pre">LeafletFinder.group()</span></code></a> and <a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter" title="MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter"><code class="xref py py-meth docutils literal"><span class="pre">LeafletFinder.groups_iter()</span></code></a></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter">
-<tt class="descname">groups_iter</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.groups_iter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter" title="Permalink to this definition">¶</a></dt>
-<dd><p>Iterator over all leaflet <a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder.groups" title="MDAnalysis.analysis.leaflet.LeafletFinder.groups"><tt class="xref py py-meth docutils literal"><span class="pre">groups()</span></tt></a></p>
+<code class="descname">groups_iter</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.groups_iter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter" title="Permalink to this definition">¶</a></dt>
+<dd><p>Iterator over all leaflet <a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder.groups" title="MDAnalysis.analysis.leaflet.LeafletFinder.groups"><code class="xref py py-meth docutils literal"><span class="pre">groups()</span></code></a></p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.leaflet.LeafletFinder.sizes">
-<tt class="descname">sizes</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.sizes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.sizes" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sizes</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.sizes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.sizes" title="Permalink to this definition">¶</a></dt>
 <dd><p>Dict of component index with size of component.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.leaflet.LeafletFinder.update">
-<tt class="descname">update</tt><big>(</big><em>cutoff=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.update"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.update" title="Permalink to this definition">¶</a></dt>
+<code class="descname">update</code><span class="sig-paren">(</span><em>cutoff=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.update"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.update" title="Permalink to this definition">¶</a></dt>
 <dd><p>Update components, possibly with a different <em>cutoff</em></p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.leaflet.LeafletFinder.write_selection">
-<tt class="descname">write_selection</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.write_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.write_selection" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_selection</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#LeafletFinder.write_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.LeafletFinder.write_selection" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write selections for the leaflets to <em>filename</em>.</p>
 <p>The format is typically determined by the extension of <em>filename</em>
 (e.g. &#8220;vmd&#8221;, &#8220;pml&#8221;, or &#8220;ndx&#8221; for VMD, PyMol, or Gromacs).</p>
-<p>See <a class="reference internal" href="../selections/base.html#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.selections.base.SelectionWriter</span></tt></a> for all
+<p>See <a class="reference internal" href="../selections/base.html#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.selections.base.SelectionWriter</span></code></a> for all
 options.</p>
 </dd></dl>
 
@@ -237,7 +237,7 @@ <h1>3.3.2. Leaflet identification &#8212; <a class="reference internal" href="#m
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.leaflet.optimize_cutoff">
-<tt class="descclassname">MDAnalysis.analysis.leaflet.</tt><tt class="descname">optimize_cutoff</tt><big>(</big><em>universe</em>, <em>selection</em>, <em>dmin=10.0</em>, <em>dmax=20.0</em>, <em>step=0.5</em>, <em>max_imbalance=0.2</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#optimize_cutoff"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.optimize_cutoff" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.leaflet.</code><code class="descname">optimize_cutoff</code><span class="sig-paren">(</span><em>universe</em>, <em>selection</em>, <em>dmin=10.0</em>, <em>dmax=20.0</em>, <em>step=0.5</em>, <em>max_imbalance=0.2</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/leaflet.html#optimize_cutoff"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.leaflet.optimize_cutoff" title="Permalink to this definition">¶</a></dt>
 <dd><p>Find cutoff that minimizes number of disconnected groups.</p>
 <p>Applies heuristics to find best groups:</p>
 <ol class="arabic">
@@ -255,12 +255,12 @@ <h1>3.3.2. Leaflet identification &#8212; <a class="reference internal" href="#m
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> instance</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> instance</p>
 </dd>
 <dt><em>selection</em></dt>
-<dd><p class="first last">selection string as used for <a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder" title="MDAnalysis.analysis.leaflet.LeafletFinder"><tt class="xref py py-class docutils literal"><span class="pre">LeafletFinder</span></tt></a></p>
+<dd><p class="first last">selection string as used for <a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder" title="MDAnalysis.analysis.leaflet.LeafletFinder"><code class="xref py py-class docutils literal"><span class="pre">LeafletFinder</span></code></a></p>
 </dd>
 <dt><em>dmin</em>, <em>dmax</em>, <em>step</em></dt>
 <dd><p class="first last">scan cutoffs from <em>dmin</em> to <em>dmax</em> at stepsize*step (in Angstroms)</p>
@@ -269,15 +269,15 @@ <h1>3.3.2. Leaflet identification &#8212; <a class="reference internal" href="#m
 <dd><p class="first last">tuning parameter for the balancing heuristic (2) [0.2]</p>
 </dd>
 <dt><em>kwargs</em></dt>
-<dd><p class="first last">other arguments for  <a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder" title="MDAnalysis.analysis.leaflet.LeafletFinder"><tt class="xref py py-class docutils literal"><span class="pre">LeafletFinder</span></tt></a></p>
+<dd><p class="first last">other arguments for  <a class="reference internal" href="#MDAnalysis.analysis.leaflet.LeafletFinder" title="MDAnalysis.analysis.leaflet.LeafletFinder"><code class="xref py py-class docutils literal"><span class="pre">LeafletFinder</span></code></a></p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first"><tt class="docutils literal"><span class="pre">(cutoff,N)</span></tt> optimum cutoff and number of groups found</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><code class="docutils literal"><span class="pre">(cutoff,N)</span></code> optimum cutoff and number of groups found</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last">can die in various ways if really no appropriate number of groups
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">can die in various ways if really no appropriate number of groups
 can be found; needs to be made more robust</p>
 </td>
 </tr>
@@ -293,7 +293,7 @@ <h1>3.3.2. Leaflet identification &#8212; <a class="reference internal" href="#m
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -308,11 +308,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="hole.html" title="3.3.1. Generation and Analysis of HOLE pore profiles — MDAnalysis.analysis.hole"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -322,7 +322,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/nuclinfo.html b/package/doc/html/documentation_pages/analysis/nuclinfo.html
index 240fceced23..eb3413a92f2 100644
--- a/package/doc/html/documentation_pages/analysis/nuclinfo.html
+++ b/package/doc/html/documentation_pages/analysis/nuclinfo.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.4.1. Nucleic acid analysis — MDAnalysis.analysis.nuclinfo &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.4.1. Nucleic acid analysis — MDAnalysis.analysis.nuclinfo &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles — MDAnalysis.analysis.x3dna" href="x3dna.html" />
     <link rel="prev" title="3.3.2. Leaflet identification — MDAnalysis.analysis.leaflet" href="leaflet.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="leaflet.html" title="3.3.2. Leaflet identification — MDAnalysis.analysis.leaflet"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.4.1. Nucleic acid analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.nuclinfo</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.4.1. Nucleic acid analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.nuclinfo</span></code></a><ul>
 <li><a class="reference internal" href="#distances">3.4.1.1. Distances</a></li>
 <li><a class="reference internal" href="#phases">3.4.1.2. Phases</a></li>
 <li><a class="reference internal" href="#dihedral-angles">3.4.1.3. Dihedral angles</a></li>
@@ -72,16 +70,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="leaflet.html"
-                        title="previous chapter">3.3.2. Leaflet identification &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.analysis.leaflet</span></tt></a></p>
+                        title="previous chapter">3.3.2. Leaflet identification &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.leaflet</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="x3dna.html"
-                        title="next chapter">3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.analysis.x3dna</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/analysis/nuclinfo.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.x3dna</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/analysis/nuclinfo.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -100,10 +100,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.nuclinfo"></span><div class="section" id="nucleic-acid-analysis-mdanalysis-analysis-nuclinfo">
-<h1>3.4.1. Nucleic acid analysis &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.nuclinfo" title="MDAnalysis.analysis.nuclinfo"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.nuclinfo</span></tt></a><a class="headerlink" href="#nucleic-acid-analysis-mdanalysis-analysis-nuclinfo" title="Permalink to this headline">¶</a></h1>
+<h1>3.4.1. Nucleic acid analysis &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.nuclinfo" title="MDAnalysis.analysis.nuclinfo"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.nuclinfo</span></code></a><a class="headerlink" href="#nucleic-acid-analysis-mdanalysis-analysis-nuclinfo" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -124,8 +124,8 @@ <h1>3.4.1. Nucleic acid analysis &#8212; <a class="reference internal" href="#mo
 <li>AS or CP phase angles,</li>
 <li>Watson-Crick N1-N3 distances, C2-O2 distances, N6-O4 distances, O6-N4 distances.</li>
 </ul>
-<p>For applications of this kind of analysis see <a class="reference internal" href="#denning2011">[Denning2011]</a> and <a class="reference internal" href="#denning2012">[Denning2012]</a>.</p>
-<p>All functions take a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> as an argument
+<p>For applications of this kind of analysis see <a class="reference internal" href="#denning2011" id="id1">[Denning2011]</a> and <a class="reference internal" href="#denning2012" id="id2">[Denning2012]</a>.</p>
+<p>All functions take a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> as an argument
 together with further parameters that specify the base or bases in question. Angles are
 in degrees. The functions use standard CHARMM names for nucleic acids and atom names.</p>
 <p class="rubric">References</p>
@@ -150,7 +150,7 @@ <h1>3.4.1. Nucleic acid analysis &#8212; <a class="reference internal" href="#mo
 <h2>3.4.1.1. Distances<a class="headerlink" href="#distances" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.wc_pair">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">wc_pair</tt><big>(</big><em>universe</em>, <em>i</em>, <em>bp</em>, <em>seg1='SYSTEM'</em>, <em>seg2='SYSTEM'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#wc_pair"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.wc_pair" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">wc_pair</code><span class="sig-paren">(</span><em>universe</em>, <em>i</em>, <em>bp</em>, <em>seg1='SYSTEM'</em>, <em>seg2='SYSTEM'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#wc_pair"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.wc_pair" title="Permalink to this definition">¶</a></dt>
 <dd><p>Watson-Crick basepair distance for residue <em>i</em> with residue <em>bp</em>.</p>
 <p>The distance of the nitrogen atoms in a Watson-Crick hydrogen bond is
 computed.</p>
@@ -158,9 +158,9 @@ <h2>3.4.1.1. Distances<a class="headerlink" href="#distances" title="Permalink t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>seg1</em></dt>
 <dd><p class="first last">segment id for first base</p>
@@ -183,13 +183,14 @@ <h2>3.4.1.1. Distances<a class="headerlink" href="#distances" title="Permalink t
 <p class="first admonition-title">Note</p>
 <p class="last">If failure occurs be sure to check the segment identification.</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.minor_pair">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">minor_pair</tt><big>(</big><em>universe</em>, <em>i</em>, <em>bp</em>, <em>seg1='SYSTEM'</em>, <em>seg2='SYSTEM'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#minor_pair"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.minor_pair" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">minor_pair</code><span class="sig-paren">(</span><em>universe</em>, <em>i</em>, <em>bp</em>, <em>seg1='SYSTEM'</em>, <em>seg2='SYSTEM'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#minor_pair"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.minor_pair" title="Permalink to this definition">¶</a></dt>
 <dd><p>Minor-Groove basepair distance for residue <em>i</em> with residue <em>bp</em>.</p>
 <p>The distance of the nitrogen and oxygen atoms in a Minor-groove hydrogen bond is
 computed.</p>
@@ -197,9 +198,9 @@ <h2>3.4.1.1. Distances<a class="headerlink" href="#distances" title="Permalink t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>seg1</em></dt>
 <dd><p class="first last">segment id for first base</p>
@@ -222,13 +223,14 @@ <h2>3.4.1.1. Distances<a class="headerlink" href="#distances" title="Permalink t
 <p class="first admonition-title">Note</p>
 <p class="last">If failure occurs be sure to check the segment identification.</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.major_pair">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">major_pair</tt><big>(</big><em>universe</em>, <em>i</em>, <em>bp</em>, <em>seg1='SYSTEM'</em>, <em>seg2='SYSTEM'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#major_pair"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.major_pair" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">major_pair</code><span class="sig-paren">(</span><em>universe</em>, <em>i</em>, <em>bp</em>, <em>seg1='SYSTEM'</em>, <em>seg2='SYSTEM'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#major_pair"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.major_pair" title="Permalink to this definition">¶</a></dt>
 <dd><p>Major-Groove basepair distance for residue <em>i</em> with residue <em>bp</em>.</p>
 <p>The distance of the nitrogen and oxygen atoms in a Major-groove hydrogen bond is
 computed.</p>
@@ -236,9 +238,9 @@ <h2>3.4.1.1. Distances<a class="headerlink" href="#distances" title="Permalink t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory       <em>i</em></p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory       <em>i</em></p>
 </dd>
 <dt><em>seg1</em></dt>
 <dd><p class="first last">segment id for first base</p>
@@ -261,8 +263,9 @@ <h2>3.4.1.1. Distances<a class="headerlink" href="#distances" title="Permalink t
 <p class="first admonition-title">Note</p>
 <p class="last">If failure occurs be sure to check the segment identification</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 </div>
@@ -270,17 +273,17 @@ <h2>3.4.1.1. Distances<a class="headerlink" href="#distances" title="Permalink t
 <h2>3.4.1.2. Phases<a class="headerlink" href="#phases" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.phase_cp">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">phase_cp</tt><big>(</big><em>universe</em>, <em>seg</em>, <em>i</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#phase_cp"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.phase_cp" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">phase_cp</code><span class="sig-paren">(</span><em>universe</em>, <em>seg</em>, <em>i</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#phase_cp"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.phase_cp" title="Permalink to this definition">¶</a></dt>
 <dd><p>Pseudo-angle describing the phase of the ribose pucker for residue <em>i</em> using the CP method.</p>
 <p>The angle is computed by the positions of atoms in the ribose ring.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><blockquote class="first">
-<div><p><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<div><p><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </div></blockquote>
 <dl class="last docutils">
 <dt><em>segid</em></dt>
@@ -296,22 +299,23 @@ <h2>3.4.1.2. Phases<a class="headerlink" href="#phases" title="Permalink to this
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.phase_as">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">phase_as</tt><big>(</big><em>universe</em>, <em>seg</em>, <em>i</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#phase_as"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.phase_as" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">phase_as</code><span class="sig-paren">(</span><em>universe</em>, <em>seg</em>, <em>i</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#phase_as"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.phase_as" title="Permalink to this definition">¶</a></dt>
 <dd><p>Pseudo-angle describing the phase of the ribose pucker for residue <em>i</em> using the AS method</p>
 <p>The angle is computed by the position vector of atoms in the ribose ring.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>segid</em></dt>
 <dd><p class="first last">segment identity of resid</p>
@@ -324,8 +328,9 @@ <h2>3.4.1.2. Phases<a class="headerlink" href="#phases" title="Permalink to this
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 </div>
@@ -333,16 +338,16 @@ <h2>3.4.1.2. Phases<a class="headerlink" href="#phases" title="Permalink to this
 <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.tors">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">tors</tt><big>(</big><em>universe</em>, <em>seg</em>, <em>i</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">tors</code><span class="sig-paren">(</span><em>universe</em>, <em>seg</em>, <em>i</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors" title="Permalink to this definition">¶</a></dt>
 <dd><p>Backbone dihedrals includes alpha, beta, gamma, delta, epsilon, zeta, chi</p>
 <p>The dihedral is computed based on position atoms for resid <em>i</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>segid</em></dt>
 <dd><p class="first last">segid of resid</p>
@@ -363,16 +368,16 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.tors_alpha">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">tors_alpha</tt><big>(</big><em>universe</em>, <em>seg</em>, <em>i</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_alpha"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_alpha" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">tors_alpha</code><span class="sig-paren">(</span><em>universe</em>, <em>seg</em>, <em>i</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_alpha"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_alpha" title="Permalink to this definition">¶</a></dt>
 <dd><p>alpha backbone dihedral</p>
 <p>The dihedral is computed based on position atoms for resid <em>i</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>segid</em></dt>
 <dd><p class="first last">segid of resid</p>
@@ -385,22 +390,23 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.tors_beta">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">tors_beta</tt><big>(</big><em>universe</em>, <em>seg</em>, <em>i</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_beta"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_beta" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">tors_beta</code><span class="sig-paren">(</span><em>universe</em>, <em>seg</em>, <em>i</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_beta"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_beta" title="Permalink to this definition">¶</a></dt>
 <dd><p>beta  backbone dihedral</p>
 <p>The dihedral is computed based on position atoms for resid <em>i</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>segid</em></dt>
 <dd><p class="first last">segid of resid</p>
@@ -413,13 +419,14 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.tors_gamma">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">tors_gamma</tt><big>(</big><em>universe</em>, <em>seg</em>, <em>i</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_gamma"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_gamma" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">tors_gamma</code><span class="sig-paren">(</span><em>universe</em>, <em>seg</em>, <em>i</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_gamma"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_gamma" title="Permalink to this definition">¶</a></dt>
 <dd><p>Gamma backbone dihedral</p>
 <blockquote>
 <div>The dihedral is computed based on position atoms for resid <em>i</em>.</div></blockquote>
@@ -427,9 +434,9 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>segid</em></dt>
 <dd><p class="first last">segid of resid</p>
@@ -442,22 +449,23 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.tors_delta">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">tors_delta</tt><big>(</big><em>universe</em>, <em>seg</em>, <em>i</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_delta"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_delta" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">tors_delta</code><span class="sig-paren">(</span><em>universe</em>, <em>seg</em>, <em>i</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_delta"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_delta" title="Permalink to this definition">¶</a></dt>
 <dd><p>delta backbone dihedral</p>
 <p>The dihedral is computed based on position atoms for resid <em>i</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>segid</em></dt>
 <dd><p class="first last">segid of resid</p>
@@ -470,22 +478,23 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.tors_eps">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">tors_eps</tt><big>(</big><em>universe</em>, <em>seg</em>, <em>i</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_eps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_eps" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">tors_eps</code><span class="sig-paren">(</span><em>universe</em>, <em>seg</em>, <em>i</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_eps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_eps" title="Permalink to this definition">¶</a></dt>
 <dd><p>Epsilon backbone dihedral</p>
 <p>The dihedral is computed based on position atoms for resid <em>i</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>segid</em></dt>
 <dd><p class="first last">segid of resid</p>
@@ -498,22 +507,23 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.tors_zeta">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">tors_zeta</tt><big>(</big><em>universe</em>, <em>seg</em>, <em>i</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_zeta"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_zeta" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">tors_zeta</code><span class="sig-paren">(</span><em>universe</em>, <em>seg</em>, <em>i</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_zeta"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_zeta" title="Permalink to this definition">¶</a></dt>
 <dd><p>Zeta backbone dihedral</p>
 <p>The dihedral is computed based on position atoms for resid <em>i</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>segid</em></dt>
 <dd><p class="first last">segid of resid</p>
@@ -526,13 +536,14 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.tors_chi">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">tors_chi</tt><big>(</big><em>universe</em>, <em>seg</em>, <em>i</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_chi"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_chi" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">tors_chi</code><span class="sig-paren">(</span><em>universe</em>, <em>seg</em>, <em>i</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#tors_chi"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.tors_chi" title="Permalink to this definition">¶</a></dt>
 <dd><p>chi nucleic acid dihedral</p>
 <blockquote>
 <div><p>The dihedral is computed based on position atoms for resid <em>i</em>.</p>
@@ -542,7 +553,7 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>segid</em></dt>
 <dd><p class="first last">segid of resid</p>
@@ -556,13 +567,14 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 </tbody>
 </table>
 </div></blockquote>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.hydroxyl">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">hydroxyl</tt><big>(</big><em>universe</em>, <em>seg</em>, <em>i</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#hydroxyl"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.hydroxyl" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">hydroxyl</code><span class="sig-paren">(</span><em>universe</em>, <em>seg</em>, <em>i</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#hydroxyl"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.hydroxyl" title="Permalink to this definition">¶</a></dt>
 <dd><p>2-hydroxyl dihedral. Useful only for RNA calculations.</p>
 <blockquote>
 <div><div class="admonition note">
@@ -576,7 +588,7 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>segid</em></dt>
 <dd><p class="first last">segid of resid</p>
@@ -590,13 +602,14 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 </tbody>
 </table>
 </div></blockquote>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.nuclinfo.pseudo_dihe_baseflip">
-<tt class="descclassname">MDAnalysis.analysis.nuclinfo.</tt><tt class="descname">pseudo_dihe_baseflip</tt><big>(</big><em>universe</em>, <em>bp1</em>, <em>bp2</em>, <em>i</em>, <em>seg1='SYSTEM'</em>, <em>seg2='SYSTEM'</em>, <em>seg3='SYSTEM'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#pseudo_dihe_baseflip"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.pseudo_dihe_baseflip" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.nuclinfo.</code><code class="descname">pseudo_dihe_baseflip</code><span class="sig-paren">(</span><em>universe</em>, <em>bp1</em>, <em>bp2</em>, <em>i</em>, <em>seg1='SYSTEM'</em>, <em>seg2='SYSTEM'</em>, <em>seg3='SYSTEM'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/nuclinfo.html#pseudo_dihe_baseflip"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.nuclinfo.pseudo_dihe_baseflip" title="Permalink to this definition">¶</a></dt>
 <dd><p>pseudo dihedral for flipped bases. Useful only for nucleic acid base flipping</p>
 <blockquote>
 <div><p>The dihedral is computed based on position atoms for resid <em>i</em></p>
@@ -611,7 +624,7 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> containing the trajectory</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> containing the trajectory</p>
 </dd>
 <dt><em>segid1</em></dt>
 <dd><p class="first last">segid of resid base pairing with bp2</p>
@@ -637,8 +650,9 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
 </tbody>
 </table>
 </div></blockquote>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.0.</span></p>
+</div>
 </dd></dl>
 
 </div>
@@ -650,7 +664,7 @@ <h2>3.4.1.3. Dihedral angles<a class="headerlink" href="#dihedral-angles" title=
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -665,11 +679,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="leaflet.html" title="3.3.2. Leaflet identification — MDAnalysis.analysis.leaflet"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -679,7 +693,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/psa.html b/package/doc/html/documentation_pages/analysis/psa.html
index 7def3f03f98..487c1b9f3d5 100644
--- a/package/doc/html/documentation_pages/analysis/psa.html
+++ b/package/doc/html/documentation_pages/analysis/psa.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.1.5. Calculating path similarity — MDAnalysis.analysis.psa &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.1.5. Calculating path similarity — MDAnalysis.analysis.psa &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="3.2.1. Hydrogen Bond analysis — MDAnalysis.analysis.hbonds.hbond_analysis" href="hbond_analysis.html" />
     <link rel="prev" title="3.1.4. Calculating root mean square quantities — MDAnalysis.analysis.rms" href="rms.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="rms.html" title="3.1.4. Calculating root mean square quantities — MDAnalysis.analysis.rms"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.1.5. Calculating path similarity &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.psa</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.1.5. Calculating path similarity &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.psa</span></code></a><ul>
 <li><a class="reference internal" href="#helper-functions-and-variables">3.1.5.1. Helper functions and variables</a></li>
 <li><a class="reference internal" href="#classes-methods-and-functions">3.1.5.2. Classes, methods, and functions</a></li>
 </ul>
@@ -71,16 +69,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="rms.html"
-                        title="previous chapter">3.1.4. Calculating root mean square quantities &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></tt></a></p>
+                        title="previous chapter">3.1.4. Calculating root mean square quantities &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="hbond_analysis.html"
-                        title="next chapter">3.2.1. Hydrogen Bond analysis &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_analysis</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/analysis/psa.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">3.2.1. Hydrogen Bond analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_analysis</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/analysis/psa.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -99,10 +99,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.psa"></span><div class="section" id="calculating-path-similarity-mdanalysis-analysis-psa">
-<h1>3.1.5. Calculating path similarity &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.psa" title="MDAnalysis.analysis.psa"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.psa</span></tt></a><a class="headerlink" href="#calculating-path-similarity-mdanalysis-analysis-psa" title="Permalink to this headline">¶</a></h1>
+<h1>3.1.5. Calculating path similarity &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.psa" title="MDAnalysis.analysis.psa"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.psa</span></code></a><a class="headerlink" href="#calculating-path-similarity-mdanalysis-analysis-psa" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -115,11 +115,12 @@ <h1>3.1.5. Calculating path similarity &#8212; <a class="reference internal" hre
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.10.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.10.0.</span></p>
+</div>
 <p>The module contains code to calculate the geometric similarity of trajectories
 using path metrics such as the Hausdorff or Fréchet distances
-<a class="reference internal" href="#seyler2015">[Seyler2015]</a>. The path metrics are functions of two paths and return a
+<a class="reference internal" href="#seyler2015" id="id1">[Seyler2015]</a>. The path metrics are functions of two paths and return a
 nonnegative number, i.e., a distance. Two paths are identical if their distance
 is zero, and large distances indicate dissimilarity. Each path metric is a
 function of the individual points (e.g., coordinate snapshots) that comprise
@@ -137,7 +138,7 @@ <h1>3.1.5. Calculating path similarity &#8212; <a class="reference internal" hre
 is necessary to preserve the metric properties of the Hausdorff and Fréchet
 metrics; using the best-fit rmsd on a pairwise basis does not generally
 preserve the triangle inequality.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">The <a class="reference external" href="https://github.com/Becksteinlab/PSAnalysisTutorial">PSAnalysisTutorial</a> outlines a typical application of PSA to
 a set of trajectories, including doing proper alignment,
@@ -159,26 +160,26 @@ <h2>3.1.5.1. Helper functions and variables<a class="headerlink" href="#helper-f
 module.</p>
 <dl class="data">
 <dt id="MDAnalysis.analysis.psa.hausdorff_names">
-<tt class="descclassname">MDAnalysis.analysis.psa.</tt><tt class="descname">hausdorff_names</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.hausdorff_names" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.psa.</code><code class="descname">hausdorff_names</code><a class="headerlink" href="#MDAnalysis.analysis.psa.hausdorff_names" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.analysis.psa.frechet_names">
-<tt class="descclassname">MDAnalysis.analysis.psa.</tt><tt class="descname">frechet_names</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.frechet_names" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.psa.</code><code class="descname">frechet_names</code><a class="headerlink" href="#MDAnalysis.analysis.psa.frechet_names" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <p>The following functions are used by the other functions in this module.</p>
 <dl class="function">
 <dt id="MDAnalysis.analysis.psa.sqnorm">
-<tt class="descclassname">MDAnalysis.analysis.psa.</tt><tt class="descname">sqnorm</tt><big>(</big><em>v</em>, <em>axis=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#sqnorm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.sqnorm" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.psa.</code><code class="descname">sqnorm</code><span class="sig-paren">(</span><em>v</em>, <em>axis=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#sqnorm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.sqnorm" title="Permalink to this definition">¶</a></dt>
 <dd><p>Compute the sum of squares of elements along specified axes.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>v</em></dt>
-<dd><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> of coordinates</p>
+<dd><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> of coordinates</p>
 </dd>
 <dt><em>axis</em></dt>
 <dd><p class="first last">None or int or tuple of ints, optional
@@ -189,7 +190,7 @@ <h2>3.1.5.1. Helper functions and variables<a class="headerlink" href="#helper-f
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">float, the sum of the squares of the elements of <em>v</em> along <em>axis</em></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">float, the sum of the squares of the elements of <em>v</em> along <em>axis</em></p>
 </td>
 </tr>
 </tbody>
@@ -201,20 +202,20 @@ <h2>3.1.5.1. Helper functions and variables<a class="headerlink" href="#helper-f
 <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes-methods-and-functions" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.analysis.psa.get_path_metric_func">
-<tt class="descclassname">MDAnalysis.analysis.psa.</tt><tt class="descname">get_path_metric_func</tt><big>(</big><em>name</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#get_path_metric_func"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.get_path_metric_func" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.psa.</code><code class="descname">get_path_metric_func</code><span class="sig-paren">(</span><em>name</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#get_path_metric_func"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.get_path_metric_func" title="Permalink to this definition">¶</a></dt>
 <dd><p>Selects a path metric function by name.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>name</em></dt>
 <dd><p class="first last">string, name of path metric</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">The path metric function specified by <em>name</em> (if found).</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The path metric function specified by <em>name</em> (if found).</p>
 </td>
 </tr>
 </tbody>
@@ -223,31 +224,31 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.psa.hausdorff">
-<tt class="descclassname">MDAnalysis.analysis.psa.</tt><tt class="descname">hausdorff</tt><big>(</big><em>P</em>, <em>Q</em>, <em>N=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#hausdorff"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.hausdorff" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.psa.</code><code class="descname">hausdorff</code><span class="sig-paren">(</span><em>P</em>, <em>Q</em>, <em>N=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#hausdorff"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.hausdorff" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate the Hausdorff distance between two paths.</p>
-<p><em>P</em> (<em>Q</em>) is a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> of <span class="math">\(N_p\)</span> (<span class="math">\(N_q\)</span>) time
+<p><em>P</em> (<em>Q</em>) is a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> of <span class="math">\(N_p\)</span> (<span class="math">\(N_q\)</span>) time
 steps, <span class="math">\(N\)</span> atoms, and <span class="math">\(3N\)</span> coordinates (e.g.,
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.coordinates()</span></tt></a>). <em>P</em> (<em>Q</em>) has
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.coordinates()</span></code></a>). <em>P</em> (<em>Q</em>) has
 either shape <span class="math">\(N_p \times N \times 3\)</span> (<span class="math">\(N_q \times N \times 3\)</span>), or <span class="math">\(N_p \times (3N)\)</span> (<span class="math">\(N_q \times (3N)\)</span>) in flattened form.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>P</em></dt>
-<dd><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> representing a path</p>
+<dd><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> representing a path</p>
 </dd>
 <dt><em>Q</em></dt>
-<dd><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> representing a path</p>
+<dd><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> representing a path</p>
 </dd>
 <dt><em>N</em></dt>
-<dd><p class="first last">int, number of atoms; if <tt class="docutils literal"><span class="pre">None</span></tt> then <em>P</em> and <em>Q</em> are each assumed to
-be a 3D <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>; else, they are 2D (flattened)</p>
+<dd><p class="first last">int, number of atoms; if <code class="docutils literal"><span class="pre">None</span></code> then <em>P</em> and <em>Q</em> are each assumed to
+be a 3D <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a>; else, they are 2D (flattened)</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">float, the Hausdorff distance between paths <em>P</em> and <em>Q</em></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">float, the Hausdorff distance between paths <em>P</em> and <em>Q</em></p>
 </td>
 </tr>
 </tbody>
@@ -275,31 +276,31 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 
 <dl class="function">
 <dt id="MDAnalysis.analysis.psa.discrete_frechet">
-<tt class="descclassname">MDAnalysis.analysis.psa.</tt><tt class="descname">discrete_frechet</tt><big>(</big><em>P</em>, <em>Q</em>, <em>N=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#discrete_frechet"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.discrete_frechet" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.psa.</code><code class="descname">discrete_frechet</code><span class="sig-paren">(</span><em>P</em>, <em>Q</em>, <em>N=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#discrete_frechet"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.discrete_frechet" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate the discrete Frechet distance between two paths.</p>
-<p><em>P</em> (<em>Q</em>) is a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> of <span class="math">\(N_p\)</span> (<span class="math">\(N_q\)</span>) time
+<p><em>P</em> (<em>Q</em>) is a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> of <span class="math">\(N_p\)</span> (<span class="math">\(N_q\)</span>) time
 steps, <span class="math">\(N\)</span> atoms, and <span class="math">\(3N\)</span> coordinates (e.g.,
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.coordinates()</span></tt></a>). <em>P</em> (<em>Q</em>) has
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.coordinates()</span></code></a>). <em>P</em> (<em>Q</em>) has
 either shape <span class="math">\(N_p \times N \times 3\)</span> (<span class="math">\(N_q \times N \times 3\)</span>), or :<span class="math">\(N_p \times (3N)\)</span> (<span class="math">\(N_q \times (3N)\)</span>) in flattened form.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>P</em></dt>
-<dd><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> representing a path</p>
+<dd><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> representing a path</p>
 </dd>
 <dt><em>Q</em></dt>
-<dd><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> representing a path</p>
+<dd><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> representing a path</p>
 </dd>
 <dt><em>N</em></dt>
-<dd><p class="first last">int, number of atoms; if <tt class="docutils literal"><span class="pre">None</span></tt> then <em>P</em> and <em>Q</em> are each assumed to
-be a 3D <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>; else, they are 2D (flattened)</p>
+<dd><p class="first last">int, number of atoms; if <code class="docutils literal"><span class="pre">None</span></code> then <em>P</em> and <em>Q</em> are each assumed to
+be a 3D <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a>; else, they are 2D (flattened)</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">float, the discrete Frechet distance between paths <em>P</em> and <em>Q</em></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">float, the discrete Frechet distance between paths <em>P</em> and <em>Q</em></p>
 </td>
 </tr>
 </tbody>
@@ -327,50 +328,51 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.psa.Path">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.psa.</tt><tt class="descname">Path</tt><big>(</big><em>universe</em>, <em>reference</em>, <em>ref_select='name CA'</em>, <em>path_select='all'</em>, <em>ref_frame=0</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#Path"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.Path" title="Permalink to this definition">¶</a></dt>
-<dd><p>Pre-process a <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object: (1) fit the
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.psa.</code><code class="descname">Path</code><span class="sig-paren">(</span><em>universe</em>, <em>reference</em>, <em>ref_select='name CA'</em>, <em>path_select='all'</em>, <em>ref_frame=0</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#Path"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.Path" title="Permalink to this definition">¶</a></dt>
+<dd><p>Pre-process a <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object: (1) fit the
 trajectory to a reference structure, (2) convert fitted time series to a
-<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> representation of <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a>.</p>
-<p>The analysis is performed with <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.run" title="MDAnalysis.analysis.psa.PSA.run"><tt class="xref py py-meth docutils literal"><span class="pre">PSA.run()</span></tt></a> and stores the result
-in the <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> distance matrix <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></tt></a>. <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.run" title="MDAnalysis.analysis.psa.PSA.run"><tt class="xref py py-meth docutils literal"><span class="pre">PSA.run()</span></tt></a>
+<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> representation of <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a>.</p>
+<p>The analysis is performed with <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.run" title="MDAnalysis.analysis.psa.PSA.run"><code class="xref py py-meth docutils literal"><span class="pre">PSA.run()</span></code></a> and stores the result
+in the <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> distance matrix <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><code class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></code></a>. <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.run" title="MDAnalysis.analysis.psa.PSA.run"><code class="xref py py-meth docutils literal"><span class="pre">PSA.run()</span></code></a>
 also generates a fitted trajectory and path from alignment of the original
 trajectories to a reference structure.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.1.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.1.</span></p>
+</div>
 <p>Setting up trajectory alignment and fitted path generation.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object containing a trajectory</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object containing a trajectory</p>
 </dd>
 <dt><em>reference</em></dt>
-<dd><p class="first last">reference structure; <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object; if
-<tt class="docutils literal"><span class="pre">None</span></tt> then <em>traj</em> is used (uses the current time step of the
-object) [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">reference structure; <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object; if
+<code class="docutils literal"><span class="pre">None</span></code> then <em>traj</em> is used (uses the current time step of the
+object) [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>ref_select</em></dt>
 <dd><p class="first">The selection to operate on for rms fitting; can be one of:</p>
 <ol class="arabic simple">
 <li>any valid selection string for
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> that
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> that
 produces identical selections in <em>mobile</em> and <em>reference</em>; or</li>
-<li>a dictionary <tt class="docutils literal"><span class="pre">{'mobile':sel1,</span> <span class="pre">'reference':sel2}</span></tt> (the
-<a class="reference internal" href="align.html#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.analysis.align.fasta2select()</span></tt></a> function returns
+<li>a dictionary <code class="docutils literal"><span class="pre">{'mobile':sel1,</span> <span class="pre">'reference':sel2}</span></code> (the
+<a class="reference internal" href="align.html#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.analysis.align.fasta2select()</span></code></a> function returns
 such a dictionary based on a <a class="reference external" href="http://www.clustal.org/">ClustalW</a> or <a class="reference external" href="http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/">STAMP</a> sequence
 alignment); or</li>
-<li>a tuple <tt class="docutils literal"><span class="pre">(sel1,</span> <span class="pre">sel2)</span></tt></li>
+<li>a tuple <code class="docutils literal"><span class="pre">(sel1,</span> <span class="pre">sel2)</span></code></li>
 </ol>
 <p class="last">When using 2. or 3. with <em>sel1</em> and <em>sel2</em> then these selections
 can also each be a list of selection strings (to generate an
 AtomGroup with defined atom order as described under
-<a class="reference internal" href="../selections.html#ordered-selections-label"><em>Ordered selections</em></a>).</p>
+<a class="reference internal" href="../selections.html#ordered-selections-label"><span>Ordered selections</span></a>).</p>
 </dd>
 <dt><em>path_select</em></dt>
-<dd><p class="first last">atom selection composing coordinates of (fitted) path; if <tt class="docutils literal"><span class="pre">None</span></tt>
-then <em>path_select</em> is set to <em>ref_select</em> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">atom selection composing coordinates of (fitted) path; if <code class="docutils literal"><span class="pre">None</span></code>
+then <em>path_select</em> is set to <em>ref_select</em> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -379,70 +381,70 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 </table>
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.Path.u_original">
-<tt class="descname">u_original</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.u_original" title="Permalink to this definition">¶</a></dt>
-<dd><p><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object with a trajectory</p>
+<code class="descname">u_original</code><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.u_original" title="Permalink to this definition">¶</a></dt>
+<dd><p><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object with a trajectory</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.Path.u_reference">
-<tt class="descname">u_reference</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.u_reference" title="Permalink to this definition">¶</a></dt>
-<dd><p><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object containing a reference structure</p>
+<code class="descname">u_reference</code><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.u_reference" title="Permalink to this definition">¶</a></dt>
+<dd><p><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object containing a reference structure</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.Path.ref_select">
-<tt class="descname">ref_select</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.ref_select" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ref_select</code><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.ref_select" title="Permalink to this definition">¶</a></dt>
 <dd><p>string, selection for
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> to select frame
-from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_reference" title="MDAnalysis.analysis.psa.Path.u_reference"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_reference</span></tt></a></p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> to select frame
+from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_reference" title="MDAnalysis.analysis.psa.Path.u_reference"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_reference</span></code></a></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.Path.path_select">
-<tt class="descname">path_select</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.path_select" title="Permalink to this definition">¶</a></dt>
+<code class="descname">path_select</code><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.path_select" title="Permalink to this definition">¶</a></dt>
 <dd><p>string, selection for
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> to select atoms
-to compose <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a></p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> to select atoms
+to compose <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.Path.ref_frame">
-<tt class="descname">ref_frame</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.ref_frame" title="Permalink to this definition">¶</a></dt>
-<dd><p>int, frame index to select frame from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_reference" title="MDAnalysis.analysis.psa.Path.u_reference"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_reference</span></tt></a></p>
+<code class="descname">ref_frame</code><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.ref_frame" title="Permalink to this definition">¶</a></dt>
+<dd><p>int, frame index to select frame from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_reference" title="MDAnalysis.analysis.psa.Path.u_reference"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_reference</span></code></a></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.Path.u_fitted">
-<tt class="descname">u_fitted</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.u_fitted" title="Permalink to this definition">¶</a></dt>
-<dd><p><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object with the fitted trajectory</p>
+<code class="descname">u_fitted</code><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.u_fitted" title="Permalink to this definition">¶</a></dt>
+<dd><p><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object with the fitted trajectory</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.Path.path">
-<tt class="descname">path</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.path" title="Permalink to this definition">¶</a></dt>
-<dd><p><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> object representation of the fitted trajectory</p>
+<code class="descname">path</code><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.path" title="Permalink to this definition">¶</a></dt>
+<dd><p><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> object representation of the fitted trajectory</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.psa.Path.fit_to_reference">
-<tt class="descname">fit_to_reference</tt><big>(</big><em>filename=None</em>, <em>prefix=''</em>, <em>postfix='_fit'</em>, <em>rmsdfile=None</em>, <em>targetdir='.'</em>, <em>mass_weighted=False</em>, <em>tol_mass=0.1</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#Path.fit_to_reference"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.fit_to_reference" title="Permalink to this definition">¶</a></dt>
+<code class="descname">fit_to_reference</code><span class="sig-paren">(</span><em>filename=None</em>, <em>prefix=''</em>, <em>postfix='_fit'</em>, <em>rmsdfile=None</em>, <em>targetdir='.'</em>, <em>mass_weighted=False</em>, <em>tol_mass=0.1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#Path.fit_to_reference"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.fit_to_reference" title="Permalink to this definition">¶</a></dt>
 <dd><p>Align each trajectory frame to the reference structure with
-<a class="reference internal" href="align.html#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.analysis.align.rms_fit_trj()</span></tt></a>.</p>
+<a class="reference internal" href="align.html#MDAnalysis.analysis.align.rms_fit_trj" title="MDAnalysis.analysis.align.rms_fit_trj"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.analysis.align.rms_fit_trj()</span></code></a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">file name for the RMS-fitted trajectory or pdb; defaults to the
-original trajectory filename (from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_original" title="MDAnalysis.analysis.psa.Path.u_original"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_original</span></tt></a>) with
+original trajectory filename (from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_original" title="MDAnalysis.analysis.psa.Path.u_original"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_original</span></code></a>) with
 <em>prefix</em> prepended</p>
 </dd>
 <dt><em>prefix</em></dt>
 <dd><p class="first last">prefix for auto-generating the new output filename</p>
 </dd>
 <dt><em>rmsdfile</em></dt>
-<dd><p class="first last">file name for writing the RMSD time series [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">file name for writing the RMSD time series [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>mass_weighted</em></dt>
 <dd><p class="first last">do a mass-weighted RMSD fit</p>
@@ -454,7 +456,7 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object containing a fitted trajectory</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object containing a fitted trajectory</p>
 </td>
 </tr>
 </tbody>
@@ -463,41 +465,41 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.psa.Path.run">
-<tt class="descname">run</tt><big>(</big><em>align=False</em>, <em>filename=None</em>, <em>postfix='_fit'</em>, <em>rmsdfile=None</em>, <em>targetdir='.'</em>, <em>mass_weighted=False</em>, <em>tol_mass=0.1</em>, <em>flat=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#Path.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>align=False</em>, <em>filename=None</em>, <em>postfix='_fit'</em>, <em>rmsdfile=None</em>, <em>targetdir='.'</em>, <em>mass_weighted=False</em>, <em>tol_mass=0.1</em>, <em>flat=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#Path.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Generate a path from a trajectory and reference structure, aligning
 to a reference structure if specified.</p>
 <p>This is a convenience method to generate a fitted trajectory from an
-inputted universe (<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_original" title="MDAnalysis.analysis.psa.Path.u_original"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_original</span></tt></a>) and reference structure
-(<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_reference" title="MDAnalysis.analysis.psa.Path.u_reference"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_reference</span></tt></a>). <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.fit_to_reference" title="MDAnalysis.analysis.psa.Path.fit_to_reference"><tt class="xref py py-meth docutils literal"><span class="pre">Path.fit_to_reference()</span></tt></a> and
-<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.to_path" title="MDAnalysis.analysis.psa.Path.to_path"><tt class="xref py py-meth docutils literal"><span class="pre">Path.to_path()</span></tt></a> are used consecutively to generate a new universe
-(<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_fitted" title="MDAnalysis.analysis.psa.Path.u_fitted"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_fitted</span></tt></a>) containing the fitted trajectory along with the
-corresponding <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a> represented as an
-<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>. The method returns a tuple of the topology name
+inputted universe (<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_original" title="MDAnalysis.analysis.psa.Path.u_original"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_original</span></code></a>) and reference structure
+(<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_reference" title="MDAnalysis.analysis.psa.Path.u_reference"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_reference</span></code></a>). <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.fit_to_reference" title="MDAnalysis.analysis.psa.Path.fit_to_reference"><code class="xref py py-meth docutils literal"><span class="pre">Path.fit_to_reference()</span></code></a> and
+<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.to_path" title="MDAnalysis.analysis.psa.Path.to_path"><code class="xref py py-meth docutils literal"><span class="pre">Path.to_path()</span></code></a> are used consecutively to generate a new universe
+(<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_fitted" title="MDAnalysis.analysis.psa.Path.u_fitted"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_fitted</span></code></a>) containing the fitted trajectory along with the
+corresponding <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a> represented as an
+<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a>. The method returns a tuple of the topology name
 and new trajectory name, which can be fed directly into an
-<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object after unpacking the tuple using the
-<tt class="docutils literal"><span class="pre">*</span></tt> operator, as in
-<tt class="docutils literal"><span class="pre">MDAnalysis.Universe(*(top_name,</span> <span class="pre">newtraj_name))</span></tt>.</p>
+<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object after unpacking the tuple using the
+<code class="docutils literal"><span class="pre">*</span></code> operator, as in
+<code class="docutils literal"><span class="pre">MDAnalysis.Universe(*(top_name,</span> <span class="pre">newtraj_name))</span></code>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>align</em></dt>
-<dd><p class="first last">Align trajectory to atom selection <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.ref_select" title="MDAnalysis.analysis.psa.Path.ref_select"><tt class="xref py py-attr docutils literal"><span class="pre">Path.ref_select</span></tt></a> of
-<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_reference" title="MDAnalysis.analysis.psa.Path.u_reference"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_reference</span></tt></a>. If <tt class="docutils literal"><span class="pre">True</span></tt>, a universe containing an
-aligned trajectory is produced with <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.fit_to_reference" title="MDAnalysis.analysis.psa.Path.fit_to_reference"><tt class="xref py py-meth docutils literal"><span class="pre">Path.fit_to_reference()</span></tt></a>
-[<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Align trajectory to atom selection <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.ref_select" title="MDAnalysis.analysis.psa.Path.ref_select"><code class="xref py py-attr docutils literal"><span class="pre">Path.ref_select</span></code></a> of
+<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_reference" title="MDAnalysis.analysis.psa.Path.u_reference"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_reference</span></code></a>. If <code class="docutils literal"><span class="pre">True</span></code>, a universe containing an
+aligned trajectory is produced with <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.fit_to_reference" title="MDAnalysis.analysis.psa.Path.fit_to_reference"><code class="xref py py-meth docutils literal"><span class="pre">Path.fit_to_reference()</span></code></a>
+[<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename for the RMS-fitted trajectory or pdb; defaults to the
-original trajectory filename (from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_original" title="MDAnalysis.analysis.psa.Path.u_original"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_original</span></tt></a>) with
+original trajectory filename (from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_original" title="MDAnalysis.analysis.psa.Path.u_original"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_original</span></code></a>) with
 <em>prefix</em> prepended</p>
 </dd>
 <dt><em>prefix</em></dt>
 <dd><p class="first last">prefix for auto-generating the new output filename</p>
 </dd>
 <dt><em>rmsdfile</em></dt>
-<dd><p class="first last">file name for writing the RMSD time series [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">file name for writing the RMSD time series [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>mass_weighted</em></dt>
 <dd><p class="first last">do a mass-weighted RMSD fit</p>
@@ -507,14 +509,14 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 than <em>tol_mass</em> [0.1]</p>
 </dd>
 <dt><em>flat</em></dt>
-<dd><p class="first last">represent <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a> with a 2D (<span class="math">\(N_p\times 3N\)</span>) <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>;
-if <tt class="docutils literal"><span class="pre">False</span></tt> then <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a> is a 3D (<span class="math">\(N_p\times N\times 3\)</span>)
-<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">represent <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a> with a 2D (<span class="math">\(N_p\times 3N\)</span>) <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a>;
+if <code class="docutils literal"><span class="pre">False</span></code> then <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a> is a 3D (<span class="math">\(N_p\times N\times 3\)</span>)
+<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">A tuple of the topology name and new trajectory name.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple of the topology name and new trajectory name.</p>
 </td>
 </tr>
 </tbody>
@@ -523,40 +525,40 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.psa.Path.to_path">
-<tt class="descname">to_path</tt><big>(</big><em>fitted=False</em>, <em>select=None</em>, <em>flat=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#Path.to_path"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.to_path" title="Permalink to this definition">¶</a></dt>
+<code class="descname">to_path</code><span class="sig-paren">(</span><em>fitted=False</em>, <em>select=None</em>, <em>flat=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#Path.to_path"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.Path.to_path" title="Permalink to this definition">¶</a></dt>
 <dd><p>Generates a coordinate time series from the fitted universe
 trajectory.</p>
 <p>Given a selection of <em>N</em> atoms from <em>select</em>, the atomic positions for
-each frame in the fitted universe (<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_fitted" title="MDAnalysis.analysis.psa.Path.u_fitted"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_fitted</span></tt></a>) trajectory
+each frame in the fitted universe (<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_fitted" title="MDAnalysis.analysis.psa.Path.u_fitted"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_fitted</span></code></a>) trajectory
 (with <span class="math">\(N_p\)</span> total frames) are appended sequentially to form a 3D or 2D
-(if <em>flat</em> is <tt class="docutils literal"><span class="pre">True</span></tt>) <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> representation of the
+(if <em>flat</em> is <code class="docutils literal"><span class="pre">True</span></code>) <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> representation of the
 fitted trajectory (with dimensions <span class="math">\(N_p\times N\times 3\)</span> or <span class="math">\(N_p\times 3N\)</span>, respectively).</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>fitted</em></dt>
-<dd><p class="first last">construct a <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a> from the <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_fitted" title="MDAnalysis.analysis.psa.Path.u_fitted"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_fitted</span></tt></a>
-trajectory; if <tt class="docutils literal"><span class="pre">False</span></tt> then <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a> is generated with
-the trajectory from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_original" title="MDAnalysis.analysis.psa.Path.u_original"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_original</span></tt></a> [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">construct a <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a> from the <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_fitted" title="MDAnalysis.analysis.psa.Path.u_fitted"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_fitted</span></code></a>
+trajectory; if <code class="docutils literal"><span class="pre">False</span></code> then <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a> is generated with
+the trajectory from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_original" title="MDAnalysis.analysis.psa.Path.u_original"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_original</span></code></a> [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>select</em></dt>
 <dd><p class="first last">the selection for constructing the coordinates of each frame in
-<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a>; if <tt class="docutils literal"><span class="pre">None</span></tt> then <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path_select" title="MDAnalysis.analysis.psa.Path.path_select"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path_select</span></tt></a>
-is used, else it is overridden by <em>select</em> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a>; if <code class="docutils literal"><span class="pre">None</span></code> then <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path_select" title="MDAnalysis.analysis.psa.Path.path_select"><code class="xref py py-attr docutils literal"><span class="pre">Path.path_select</span></code></a>
+is used, else it is overridden by <em>select</em> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>flat</em></dt>
-<dd><p class="first last">represent <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a> as a 2D (<span class="math">\(N_p\times 3N\)</span>) <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>; if
-<tt class="docutils literal"><span class="pre">False</span></tt> then <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a> is a 3D (<span class="math">\(N_p\times N\times 3\)</span>)
-<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">represent <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a> as a 2D (<span class="math">\(N_p\times 3N\)</span>) <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a>; if
+<code class="docutils literal"><span class="pre">False</span></code> then <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a> is a 3D (<span class="math">\(N_p\times N\times 3\)</span>)
+<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> representing a time series of atomic positions
-of an <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> selection from
-<tt class="xref py py-attr docutils literal"><span class="pre">Path.u_fitted.trajectory</span></tt></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> representing a time series of atomic positions
+of an <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> selection from
+<code class="xref py py-attr docutils literal"><span class="pre">Path.u_fitted.trajectory</span></code></p>
 </td>
 </tr>
 </tbody>
@@ -567,14 +569,15 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.psa.PSA">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.psa.</tt><tt class="descname">PSA</tt><big>(</big><em>universes</em>, <em>reference=None</em>, <em>ref_select='name CA'</em>, <em>ref_frame=0</em>, <em>path_select=None</em>, <em>labels=None</em>, <em>targetdir=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.psa.</code><code class="descname">PSA</code><span class="sig-paren">(</span><em>universes</em>, <em>reference=None</em>, <em>ref_select='name CA'</em>, <em>ref_frame=0</em>, <em>path_select=None</em>, <em>labels=None</em>, <em>targetdir=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA" title="Permalink to this definition">¶</a></dt>
 <dd><p>Perform Path Similarity Analysis (PSA) on a set of trajectories.</p>
-<p>The analysis is performed with <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.run" title="MDAnalysis.analysis.psa.PSA.run"><tt class="xref py py-meth docutils literal"><span class="pre">PSA.run()</span></tt></a> and stores the result
-in the <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> distance matrix <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></tt></a>. <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.run" title="MDAnalysis.analysis.psa.PSA.run"><tt class="xref py py-meth docutils literal"><span class="pre">PSA.run()</span></tt></a>
+<p>The analysis is performed with <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.run" title="MDAnalysis.analysis.psa.PSA.run"><code class="xref py py-meth docutils literal"><span class="pre">PSA.run()</span></code></a> and stores the result
+in the <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> distance matrix <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><code class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></code></a>. <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.run" title="MDAnalysis.analysis.psa.PSA.run"><code class="xref py py-meth docutils literal"><span class="pre">PSA.run()</span></code></a>
 also generates a fitted trajectory and path from alignment of the original
 trajectories to a reference structure.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
 <p>Setting up Path Similarity Analysis.</p>
 <p>The mutual similarity between all unique pairs of trajectories
 are computed using a selected path metric.</p>
@@ -582,35 +585,35 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universes</em></dt>
-<dd><p class="first last">a list of universes (<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object), each
+<dd><p class="first last">a list of universes (<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object), each
 containing a trajectory</p>
 </dd>
 <dt><em>reference</em></dt>
-<dd><p class="first last">reference coordinates; <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object; if
-<tt class="docutils literal"><span class="pre">None</span></tt> the first time step of the first item in <em>trajs</em> is used
-[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">reference coordinates; <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object; if
+<code class="docutils literal"><span class="pre">None</span></code> the first time step of the first item in <em>trajs</em> is used
+[<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>ref_select</em></dt>
 <dd><p class="first">The selection to operate on; can be one of:</p>
 <ol class="arabic simple">
 <li>any valid selection string for
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> that
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> that
 produces identical selections in <em>mobile</em> and <em>reference</em>; or</li>
-<li>a dictionary <tt class="docutils literal"><span class="pre">{'mobile':sel1,</span> <span class="pre">'reference':sel2}</span></tt> (the
-<a class="reference internal" href="align.html#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.analysis.align.fasta2select()</span></tt></a> function returns
+<li>a dictionary <code class="docutils literal"><span class="pre">{'mobile':sel1,</span> <span class="pre">'reference':sel2}</span></code> (the
+<a class="reference internal" href="align.html#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.analysis.align.fasta2select()</span></code></a> function returns
 such a dictionary based on a <a class="reference external" href="http://www.clustal.org/">ClustalW</a> or <a class="reference external" href="http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/">STAMP</a> sequence
 alignment); or</li>
-<li>a tuple <tt class="docutils literal"><span class="pre">(sel1,</span> <span class="pre">sel2)</span></tt></li>
+<li>a tuple <code class="docutils literal"><span class="pre">(sel1,</span> <span class="pre">sel2)</span></code></li>
 </ol>
 <p class="last">When using 2. or 3. with <em>sel1</em> and <em>sel2</em> then these selections
 can also each be a list of selection strings (to generate an
 AtomGroup with defined atom order as described under
-<a class="reference internal" href="../selections.html#ordered-selections-label"><em>Ordered selections</em></a>).</p>
+<a class="reference internal" href="../selections.html#ordered-selections-label"><span>Ordered selections</span></a>).</p>
 </dd>
 <dt><em>mass_weighted</em></dt>
-<dd><p class="first last">do a mass-weighted RMSD fit [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">do a mass-weighted RMSD fit [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>tol_mass</em></dt>
 <dd><p class="first last">Reject match if the atomic masses for matched atoms differ by more
@@ -620,16 +623,16 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 <dd><p class="first last">frame index to select frame from <em>reference</em> [0]</p>
 </dd>
 <dt><em>path_select</em></dt>
-<dd><p class="first last">atom selection composing coordinates of (fitted) path; if <tt class="docutils literal"><span class="pre">None</span></tt>
-then <em>path_select</em> is set to <em>ref_select</em> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">atom selection composing coordinates of (fitted) path; if <code class="docutils literal"><span class="pre">None</span></code>
+then <em>path_select</em> is set to <em>ref_select</em> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>targetdir</em></dt>
 <dd><p class="first last">output files are saved there [.]</p>
 </dd>
 <dt><em>labels</em></dt>
 <dd><p class="first last">list of strings, names of trajectories to be analyzed
-(<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt>); if <tt class="docutils literal"><span class="pre">None</span></tt>, defaults to trajectory
-names [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+(<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code>); if <code class="docutils literal"><span class="pre">None</span></code>, defaults to trajectory
+names [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -638,71 +641,71 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 </table>
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.PSA.universes">
-<tt class="descname">universes</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.universes" title="Permalink to this definition">¶</a></dt>
-<dd><p>list of <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> objects containing trajectories</p>
+<code class="descname">universes</code><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.universes" title="Permalink to this definition">¶</a></dt>
+<dd><p>list of <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> objects containing trajectories</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.PSA.u_reference">
-<tt class="descname">u_reference</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.u_reference" title="Permalink to this definition">¶</a></dt>
-<dd><p><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object containing a reference structure</p>
+<code class="descname">u_reference</code><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.u_reference" title="Permalink to this definition">¶</a></dt>
+<dd><p><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object containing a reference structure</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.PSA.ref_select">
-<tt class="descname">ref_select</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.ref_select" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ref_select</code><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.ref_select" title="Permalink to this definition">¶</a></dt>
 <dd><p>string, selection for
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> to select frame
-from <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.u_reference" title="MDAnalysis.analysis.psa.PSA.u_reference"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.u_reference</span></tt></a></p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> to select frame
+from <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.u_reference" title="MDAnalysis.analysis.psa.PSA.u_reference"><code class="xref py py-attr docutils literal"><span class="pre">PSA.u_reference</span></code></a></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.PSA.path_select">
-<tt class="descname">path_select</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.path_select" title="Permalink to this definition">¶</a></dt>
+<code class="descname">path_select</code><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.path_select" title="Permalink to this definition">¶</a></dt>
 <dd><p>string, selection for
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> to select atoms
-to compose <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a></p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> to select atoms
+to compose <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.PSA.ref_frame">
-<tt class="descname">ref_frame</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.ref_frame" title="Permalink to this definition">¶</a></dt>
-<dd><p>int, frame index to select frame from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_reference" title="MDAnalysis.analysis.psa.Path.u_reference"><tt class="xref py py-attr docutils literal"><span class="pre">Path.u_reference</span></tt></a></p>
+<code class="descname">ref_frame</code><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.ref_frame" title="Permalink to this definition">¶</a></dt>
+<dd><p>int, frame index to select frame from <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.u_reference" title="MDAnalysis.analysis.psa.Path.u_reference"><code class="xref py py-attr docutils literal"><span class="pre">Path.u_reference</span></code></a></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.PSA.filename">
-<tt class="descname">filename</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.filename" title="Permalink to this definition">¶</a></dt>
-<dd><p>string, name of file to store calculated distance matrix (<a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></tt></a>)</p>
+<code class="descname">filename</code><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.filename" title="Permalink to this definition">¶</a></dt>
+<dd><p>string, name of file to store calculated distance matrix (<a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><code class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></code></a>)</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.PSA.paths">
-<tt class="descname">paths</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.paths" title="Permalink to this definition">¶</a></dt>
-<dd><p>list of <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> objects representing the set/ensemble of
+<code class="descname">paths</code><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.paths" title="Permalink to this definition">¶</a></dt>
+<dd><p>list of <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> objects representing the set/ensemble of
 fitted trajectories</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.psa.PSA.D">
-<tt class="descname">D</tt><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.D" title="Permalink to this definition">¶</a></dt>
-<dd><p>string, name of file to store calculated distance matrix (<a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></tt></a>)</p>
+<code class="descname">D</code><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.D" title="Permalink to this definition">¶</a></dt>
+<dd><p>string, name of file to store calculated distance matrix (<a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><code class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></code></a>)</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.psa.PSA.cluster">
-<tt class="descname">cluster</tt><big>(</big><em>distArray</em>, <em>method='ward'</em>, <em>count_sort=False</em>, <em>distance_sort=False</em>, <em>no_labels=True</em>, <em>color_threshold=4</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.cluster"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.cluster" title="Permalink to this definition">¶</a></dt>
+<code class="descname">cluster</code><span class="sig-paren">(</span><em>distArray</em>, <em>method='ward'</em>, <em>count_sort=False</em>, <em>distance_sort=False</em>, <em>no_labels=True</em>, <em>color_threshold=4</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.cluster"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.cluster" title="Permalink to this definition">¶</a></dt>
 <dd><p>Cluster trajectories.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>method</em></dt>
-<dd><p class="first last">string, name of linkage criterion for clustering [<tt class="docutils literal"><span class="pre">'ward'</span></tt>]</p>
+<dd><p class="first last">string, name of linkage criterion for clustering [<code class="docutils literal"><span class="pre">'ward'</span></code>]</p>
 </dd>
 <dt><em>no_labels</em></dt>
-<dd><p class="first last">boolean, if <tt class="docutils literal"><span class="pre">True</span></tt> then do not label dendrogram [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">boolean, if <code class="docutils literal"><span class="pre">True</span></code> then do not label dendrogram [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 <dt><em>color_threshold</em></dt>
 <dd><p class="first last">For brevity, let t be the color_threshold. Colors all the
@@ -712,12 +715,12 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 colored blue. If t is less than or equal to zero, all nodes are
 colored blue. If color_threshold is None or ‘default’,
 corresponding with MATLAB(TM) behavior, the threshold is set to
-0.7*max(Z[:,2]). [<tt class="docutils literal"><span class="pre">4</span></tt>]]</p>
+0.7*max(Z[:,2]). [<code class="docutils literal"><span class="pre">4</span></code>]]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">list of indices representing the row-wise order of the objects
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">list of indices representing the row-wise order of the objects
 after clustering</p>
 </td>
 </tr>
@@ -727,20 +730,20 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.psa.PSA.generate_paths">
-<tt class="descname">generate_paths</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.generate_paths"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.generate_paths" title="Permalink to this definition">¶</a></dt>
+<code class="descname">generate_paths</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.generate_paths"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.generate_paths" title="Permalink to this definition">¶</a></dt>
 <dd><p>Generate paths, aligning each to reference structure if necessary.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>align</em></dt>
-<dd><p class="first last">Align trajectories to atom selection <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.ref_select" title="MDAnalysis.analysis.psa.PSA.ref_select"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.ref_select</span></tt></a> of
-<a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.u_reference" title="MDAnalysis.analysis.psa.PSA.u_reference"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.u_reference</span></tt></a> [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Align trajectories to atom selection <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.ref_select" title="MDAnalysis.analysis.psa.PSA.ref_select"><code class="xref py py-attr docutils literal"><span class="pre">PSA.ref_select</span></code></a> of
+<a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.u_reference" title="MDAnalysis.analysis.psa.PSA.u_reference"><code class="xref py py-attr docutils literal"><span class="pre">PSA.u_reference</span></code></a> [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>filename</em></dt>
 <dd><p class="first last">strings representing base filename for fitted trajectories and
-paths [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+paths [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>infix</em></dt>
 <dd><p class="first last">additional tag string that is inserted into the output filename of
@@ -757,17 +760,17 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 <dd><p class="first last">frame index to select frame from <em>reference</em></p>
 </dd>
 <dt><em>flat</em></dt>
-<dd><p class="first last">represent <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a> as a 2D (<span class="math">\(N_p\times 3N\)</span>) <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>; if
-<tt class="docutils literal"><span class="pre">False</span></tt> then <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><tt class="xref py py-attr docutils literal"><span class="pre">Path.path</span></tt></a> is a 3D (<span class="math">\(N_p\times N\times 3\)</span>)
-<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">represent <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a> as a 2D (<span class="math">\(N_p\times 3N\)</span>) <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a>; if
+<code class="docutils literal"><span class="pre">False</span></code> then <a class="reference internal" href="#MDAnalysis.analysis.psa.Path.path" title="MDAnalysis.analysis.psa.Path.path"><code class="xref py py-attr docutils literal"><span class="pre">Path.path</span></code></a> is a 3D (<span class="math">\(N_p\times N\times 3\)</span>)
+<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>save</em></dt>
-<dd><p class="first last">boolean; if <tt class="docutils literal"><span class="pre">True</span></tt>, pickle list of names for fitted trajectories
-[<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">boolean; if <code class="docutils literal"><span class="pre">True</span></code>, pickle list of names for fitted trajectories
+[<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 <dt><em>store</em></dt>
-<dd><p class="first last">boolean; if <tt class="docutils literal"><span class="pre">True</span></tt> then writes each path (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>)
-in <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.paths" title="MDAnalysis.analysis.psa.PSA.paths"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.paths</span></tt></a> to compressed npz (numpy) files [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">boolean; if <code class="docutils literal"><span class="pre">True</span></code> then writes each path (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a>)
+in <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.paths" title="MDAnalysis.analysis.psa.PSA.paths"><code class="xref py py-attr docutils literal"><span class="pre">PSA.paths</span></code></a> to compressed npz (numpy) files [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -775,44 +778,44 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 </tbody>
 </table>
 <p>The fitted trajectories are written to new files in the
-&#8220;/trj_fit&#8221; subdirectory in <tt class="xref py py-attr docutils literal"><span class="pre">PSA.targetdir</span></tt> named
+&#8220;/trj_fit&#8221; subdirectory in <code class="xref py py-attr docutils literal"><span class="pre">PSA.targetdir</span></code> named
 &#8220;filename(<em>trajectory</em>)XXX*infix*_psa&#8221;, where &#8220;XXX&#8221; is a number between
 000 and 999; the extension of each file is the same as its original.
 Optionally, the trajectories can also be saved in numpy compressed npz
-format in the &#8220;/paths&#8221; subdirectory in <tt class="xref py py-attr docutils literal"><span class="pre">PSA.targetdir</span></tt> for
-persistence and can be accessed as the attribute <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.paths" title="MDAnalysis.analysis.psa.PSA.paths"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.paths</span></tt></a>.</p>
+format in the &#8220;/paths&#8221; subdirectory in <code class="xref py py-attr docutils literal"><span class="pre">PSA.targetdir</span></code> for
+persistence and can be accessed as the attribute <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.paths" title="MDAnalysis.analysis.psa.PSA.paths"><code class="xref py py-attr docutils literal"><span class="pre">PSA.paths</span></code></a>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.psa.PSA.load">
-<tt class="descname">load</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.load"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.load" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.load"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.load" title="Permalink to this definition">¶</a></dt>
 <dd><p>Load fitted paths specified by &#8216;psa_path-names.pkl&#8217; in
-<tt class="xref py py-attr docutils literal"><span class="pre">PSA.targetdir</span></tt>.</p>
+<code class="xref py py-attr docutils literal"><span class="pre">PSA.targetdir</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.psa.PSA.plot">
-<tt class="descname">plot</tt><big>(</big><em>filename=None</em>, <em>linkage='ward'</em>, <em>count_sort=False</em>, <em>distance_sort=False</em>, <em>figsize=4.5</em>, <em>labelsize=12</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.plot" title="Permalink to this definition">¶</a></dt>
+<code class="descname">plot</code><span class="sig-paren">(</span><em>filename=None</em>, <em>linkage='ward'</em>, <em>count_sort=False</em>, <em>distance_sort=False</em>, <em>figsize=4.5</em>, <em>labelsize=12</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.plot" title="Permalink to this definition">¶</a></dt>
 <dd><p>Plot a clustered distance matrix using method <em>linkage</em> along with
 the corresponding dendrogram. Rows (and columns) are identified using
-the list of strings specified by <tt class="xref py py-attr docutils literal"><span class="pre">PSA.labels</span></tt>.</p>
+the list of strings specified by <code class="xref py py-attr docutils literal"><span class="pre">PSA.labels</span></code>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
-<dd><p class="first last">string, save figure to <em>filename</em> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">string, save figure to <em>filename</em> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>linkage</em></dt>
-<dd><p class="first last">string, name of linkage criterion for clustering [<tt class="docutils literal"><span class="pre">'ward'</span></tt>]</p>
+<dd><p class="first last">string, name of linkage criterion for clustering [<code class="docutils literal"><span class="pre">'ward'</span></code>]</p>
 </dd>
 <dt><em>figsize</em></dt>
-<dd><p class="first last">set the vertical size of plot in inches [<tt class="docutils literal"><span class="pre">6</span></tt>]</p>
+<dd><p class="first last">set the vertical size of plot in inches [<code class="docutils literal"><span class="pre">6</span></code>]</p>
 </dd>
 <dt><em>labelsize</em></dt>
 <dd><p class="first last">set the font size for colorbar labels; font size for path labels on
-dendrogram default to 3 points smaller [<tt class="docutils literal"><span class="pre">12</span></tt>]</p>
+dendrogram default to 3 points smaller [<code class="docutils literal"><span class="pre">12</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -821,35 +824,35 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 </table>
 <p>If <em>filename</em> is supplied then the figure is also written to file (the
 suffix determines the file type, e.g. pdf, png, eps, ...). All other
-keyword arguments are passed on to <tt class="xref py py-func docutils literal"><span class="pre">pylab.imshow()</span></tt>.</p>
+keyword arguments are passed on to <code class="xref py py-func docutils literal"><span class="pre">pylab.imshow()</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.psa.PSA.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Perform path similarity analysis on the trajectories to compute
 the distance matrix.</p>
 <p>A number of parameters can be changed from the defaults. The
-result is stored as the array <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></tt></a>.</p>
+result is stored as the array <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><code class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></code></a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>metric</em></dt>
 <dd><p class="first last">selection string specifying the path metric to measure pairwise
-distances among <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.paths" title="MDAnalysis.analysis.psa.PSA.paths"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.paths</span></tt></a> [<tt class="docutils literal"><span class="pre">'hausdorff'</span></tt>]</p>
+distances among <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.paths" title="MDAnalysis.analysis.psa.PSA.paths"><code class="xref py py-attr docutils literal"><span class="pre">PSA.paths</span></code></a> [<code class="docutils literal"><span class="pre">'hausdorff'</span></code>]</p>
 </dd>
 <dt><em>start</em>, <em>stop</em>, <em>step</em></dt>
 <dd><p class="first last">start and stop frame index with step size: analyze
-<tt class="docutils literal"><span class="pre">trajectory[start:stop:step]</span></tt> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<code class="docutils literal"><span class="pre">trajectory[start:stop:step]</span></code> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>store</em></dt>
-<dd><p class="first last">boolean; if <tt class="docutils literal"><span class="pre">True</span></tt> then writes <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></tt></a> to text and
-compressed npz (numpy) files [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">boolean; if <code class="docutils literal"><span class="pre">True</span></code> then writes <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><code class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></code></a> to text and
+compressed npz (numpy) files [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 <dt><em>filename</em></dt>
-<dd><p class="first last">string, filename to save <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></tt></a></p>
+<dd><p class="first last">string, filename to save <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><code class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></code></a></p>
 </dd>
 </dl>
 </td>
@@ -860,46 +863,46 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.psa.PSA.save_paths">
-<tt class="descname">save_paths</tt><big>(</big><em>filename=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.save_paths"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.save_paths" title="Permalink to this definition">¶</a></dt>
-<dd><p>Save fitted <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.paths" title="MDAnalysis.analysis.psa.PSA.paths"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.paths</span></tt></a> to numpy compressed npz files.</p>
+<code class="descname">save_paths</code><span class="sig-paren">(</span><em>filename=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.save_paths"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.save_paths" title="Permalink to this definition">¶</a></dt>
+<dd><p>Save fitted <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.paths" title="MDAnalysis.analysis.psa.PSA.paths"><code class="xref py py-attr docutils literal"><span class="pre">PSA.paths</span></code></a> to numpy compressed npz files.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
-<dd><p class="first last">string, specifies filename [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">string, specifies filename [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p>The data are saved with <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.savez_compressed.html#numpy.savez_compressed" title="(in NumPy v1.9)"><tt class="xref py py-func docutils literal"><span class="pre">numpy.savez_compressed()</span></tt></a> in the directory
-specified by <tt class="xref py py-attr docutils literal"><span class="pre">PSA.targetdir</span></tt>.</p>
+<p>The data are saved with <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.savez_compressed.html#numpy.savez_compressed" title="(in NumPy v1.9)"><code class="xref py py-func docutils literal"><span class="pre">numpy.savez_compressed()</span></code></a> in the directory
+specified by <code class="xref py py-attr docutils literal"><span class="pre">PSA.targetdir</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.psa.PSA.save_result">
-<tt class="descname">save_result</tt><big>(</big><em>filename=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.save_result"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.save_result" title="Permalink to this definition">¶</a></dt>
-<dd><p>Save distance matrix <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><tt class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></tt></a> to a numpy compressed npz file and
+<code class="descname">save_result</code><span class="sig-paren">(</span><em>filename=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/psa.html#PSA.save_result"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.psa.PSA.save_result" title="Permalink to this definition">¶</a></dt>
+<dd><p>Save distance matrix <a class="reference internal" href="#MDAnalysis.analysis.psa.PSA.D" title="MDAnalysis.analysis.psa.PSA.D"><code class="xref py py-attr docutils literal"><span class="pre">PSA.D</span></code></a> to a numpy compressed npz file and
 text file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
-<dd><p class="first last">string, specifies filename [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">string, specifies filename [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p>The data are saved with <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.savez_compressed.html#numpy.savez_compressed" title="(in NumPy v1.9)"><tt class="xref py py-func docutils literal"><span class="pre">numpy.savez_compressed()</span></tt></a> and
-<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.savetxt.html#numpy.savetxt" title="(in NumPy v1.9)"><tt class="xref py py-func docutils literal"><span class="pre">numpy.savetxt()</span></tt></a> in the directory specified by
-<tt class="xref py py-attr docutils literal"><span class="pre">PSA.targetdir</span></tt>.</p>
+<p>The data are saved with <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.savez_compressed.html#numpy.savez_compressed" title="(in NumPy v1.9)"><code class="xref py py-func docutils literal"><span class="pre">numpy.savez_compressed()</span></code></a> and
+<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.savetxt.html#numpy.savetxt" title="(in NumPy v1.9)"><code class="xref py py-func docutils literal"><span class="pre">numpy.savetxt()</span></code></a> in the directory specified by
+<code class="xref py py-attr docutils literal"><span class="pre">PSA.targetdir</span></code>.</p>
 </dd></dl>
 
 </dd></dl>
@@ -913,7 +916,7 @@ <h2>3.1.5.2. Classes, methods, and functions<a class="headerlink" href="#classes
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -928,11 +931,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="rms.html" title="3.1.4. Calculating root mean square quantities — MDAnalysis.analysis.rms"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -942,7 +945,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/rms.html b/package/doc/html/documentation_pages/analysis/rms.html
index 355ebfc0701..4d88c34880e 100644
--- a/package/doc/html/documentation_pages/analysis/rms.html
+++ b/package/doc/html/documentation_pages/analysis/rms.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.1.4. Calculating root mean square quantities — MDAnalysis.analysis.rms &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.1.4. Calculating root mean square quantities — MDAnalysis.analysis.rms &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="3.1.5. Calculating path similarity — MDAnalysis.analysis.psa" href="psa.html" />
     <link rel="prev" title="3.1.3. Distance analysis — MDAnalysis.analysis.distances" href="distances.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="distances.html" title="3.1.3. Distance analysis — MDAnalysis.analysis.distances"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
       </ul>
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.1.4. Calculating root mean square quantities &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.1.4. Calculating root mean square quantities &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></code></a><ul>
 <li><a class="reference internal" href="#examples">3.1.4.1. Examples</a><ul>
 <li><a class="reference internal" href="#calculating-rmsd-for-multiple-domains">3.1.4.1.1. Calculating RMSD for multiple domains</a></li>
 </ul>
@@ -75,16 +73,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="distances.html"
-                        title="previous chapter">3.1.3. Distance analysis &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.analysis.distances</span></tt></a></p>
+                        title="previous chapter">3.1.3. Distance analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.distances</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="psa.html"
-                        title="next chapter">3.1.5. Calculating path similarity &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.analysis.psa</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/analysis/rms.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">3.1.5. Calculating path similarity &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.psa</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/analysis/rms.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -103,10 +103,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.rms"></span><div class="section" id="calculating-root-mean-square-quantities-mdanalysis-analysis-rms">
-<h1>3.1.4. Calculating root mean square quantities &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.rms" title="MDAnalysis.analysis.rms"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></tt></a><a class="headerlink" href="#calculating-root-mean-square-quantities-mdanalysis-analysis-rms" title="Permalink to this headline">¶</a></h1>
+<h1>3.1.4. Calculating root mean square quantities &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.rms" title="MDAnalysis.analysis.rms"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></code></a><a class="headerlink" href="#calculating-root-mean-square-quantities-mdanalysis-analysis-rms" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -119,24 +119,26 @@ <h1>3.1.4. Calculating root mean square quantities &#8212; <a class="reference i
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Added <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSF" title="MDAnalysis.analysis.rms.RMSF"><tt class="xref py py-class docutils literal"><span class="pre">RMSF</span></tt></a> analysis.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Added <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSF" title="MDAnalysis.analysis.rms.RMSF"><code class="xref py py-class docutils literal"><span class="pre">RMSF</span></code></a> analysis.</p>
+</div>
 <p>The module contains code to analyze root mean square quantities such
-as the coordinat root mean square distance (<a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD" title="MDAnalysis.analysis.rms.RMSD"><tt class="xref py py-class docutils literal"><span class="pre">RMSD</span></tt></a>) or the
-per-residue root mean square fluctuations (<a class="reference internal" href="#MDAnalysis.analysis.rms.RMSF" title="MDAnalysis.analysis.rms.RMSF"><tt class="xref py py-class docutils literal"><span class="pre">RMSF</span></tt></a>).</p>
-<p>This module uses the fast QCP algorithm <a class="reference internal" href="../lib/qcprot.html#theobald2005">[Theobald2005]</a> to calculate
+as the coordinat root mean square distance (<a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD" title="MDAnalysis.analysis.rms.RMSD"><code class="xref py py-class docutils literal"><span class="pre">RMSD</span></code></a>) or the
+per-residue root mean square fluctuations (<a class="reference internal" href="#MDAnalysis.analysis.rms.RMSF" title="MDAnalysis.analysis.rms.RMSF"><code class="xref py py-class docutils literal"><span class="pre">RMSF</span></code></a>).</p>
+<p>This module uses the fast QCP algorithm <a class="reference internal" href="../lib/qcprot.html#theobald2005" id="id1">[Theobald2005]</a> to calculate
 the root mean square distance (RMSD) between two coordinate sets (as
 implemented in
-<a class="reference internal" href="../lib/qcprot.html#MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix" title="MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix()</span></tt></a>).</p>
-<p>When using this module in published work please cite <a class="reference internal" href="../lib/qcprot.html#theobald2005">[Theobald2005]</a>.</p>
-<div class="admonition-see-also admonition seealso">
+<a class="reference internal" href="../lib/qcprot.html#MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix" title="MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix()</span></code></a>).</p>
+<p>When using this module in published work please cite <a class="reference internal" href="../lib/qcprot.html#theobald2005" id="id2">[Theobald2005]</a>.</p>
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <dl class="last docutils">
-<dt><a class="reference internal" href="align.html#module-MDAnalysis.analysis.align" title="MDAnalysis.analysis.align"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.align</span></tt></a></dt>
+<dt><a class="reference internal" href="align.html#module-MDAnalysis.analysis.align" title="MDAnalysis.analysis.align"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.align</span></code></a></dt>
 <dd>aligning structures based on RMSD</dd>
-<dt><a class="reference internal" href="../lib/qcprot.html#module-MDAnalysis.lib.qcprot" title="MDAnalysis.lib.qcprot"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></tt></a></dt>
+<dt><a class="reference internal" href="../lib/qcprot.html#module-MDAnalysis.lib.qcprot" title="MDAnalysis.lib.qcprot"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></code></a></dt>
 <dd>implements the fast RMSD algorithm.</dd>
 </dl>
 </div>
@@ -156,7 +158,7 @@ <h3>3.1.4.1.1. Calculating RMSD for multiple domains<a class="headerlink" href="
 <li>calculate the backbone RMSD and RMSD for CORE, LID, NMP (backbone atoms)</li>
 </ul>
 <p>The trajectory is included with the test data files. The data in
-<a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.rmsd" title="MDAnalysis.analysis.rms.RMSD.rmsd"><tt class="xref py py-attr docutils literal"><span class="pre">RMSD.rmsd</span></tt></a> is plotted with <a class="reference external" href="http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.plot" title="(in Matplotlib v1.4.3)"><tt class="xref py py-func docutils literal"><span class="pre">matplotlib.pyplot.plot()</span></tt></a>:</p>
+<a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.rmsd" title="MDAnalysis.analysis.rms.RMSD.rmsd"><code class="xref py py-attr docutils literal"><span class="pre">RMSD.rmsd</span></code></a> is plotted with <a class="reference external" href="http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.plot" title="(in Matplotlib v1.4.3)"><code class="xref py py-func docutils literal"><span class="pre">matplotlib.pyplot.plot()</span></code></a>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">MDAnalysis</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis.tests.datafiles</span> <span class="kn">import</span> <span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span><span class="p">,</span><span class="n">CRD</span>
 <span class="n">u</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span><span class="p">)</span>
@@ -195,23 +197,23 @@ <h3>3.1.4.1.1. Calculating RMSD for multiple domains<a class="headerlink" href="
 <h2>3.1.4.2. Functions<a class="headerlink" href="#functions" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.analysis.rms.rmsd">
-<tt class="descclassname">MDAnalysis.analysis.rms.</tt><tt class="descname">rmsd</tt><big>(</big><em>a</em>, <em>b</em>, <em>weights=None</em>, <em>center=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#rmsd"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.rmsd" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.analysis.rms.</code><code class="descname">rmsd</code><span class="sig-paren">(</span><em>a</em>, <em>b</em>, <em>weights=None</em>, <em>center=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#rmsd"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.rmsd" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns RMSD between two coordinate sets <em>a</em> and <em>b</em>.</p>
 <p><em>a</em> and <em>b</em> are arrays of the coordinates of N atoms of shape N*3
 as generated by, e.g.,
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.coordinates()</span></tt></a>.</p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.coordinates()</span></code></a>.</p>
 <p>An implicit optimal superposition is performed, which minimizes
 the RMSD between <em>a</em> and <em>b</em> although both <em>a</em> and <em>b</em> must be
 centered on the origin before performing the RMSD calculation so
 that translations are removed.</p>
-<p>One can use the <em>center</em> = <tt class="docutils literal"><span class="pre">True</span></tt> keyword, which subtracts the
-center of geometry (for <em>weights</em> = <tt class="docutils literal"><span class="pre">None</span></tt>) before the
+<p>One can use the <em>center</em> = <code class="docutils literal"><span class="pre">True</span></code> keyword, which subtracts the
+center of geometry (for <em>weights</em> = <code class="docutils literal"><span class="pre">None</span></code>) before the
 superposition. With <em>weights</em>, a weighted average is computed as
 the center.</p>
 <p>The <em>weights</em> can be an array of length N, containing e.g. masses
 for a weighted RMSD calculation.</p>
 <p>The function uses Douglas Theobald&#8217;s fast QCP algorithm
-<a class="reference internal" href="../lib/qcprot.html#theobald2005">[Theobald2005]</a> to calculate the RMSD.</p>
+<a class="reference internal" href="../lib/qcprot.html#theobald2005" id="id3">[Theobald2005]</a> to calculate the RMSD.</p>
 <dl class="docutils">
 <dt>Example::</dt>
 <dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">u</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span><span class="p">)</span>
@@ -232,16 +234,18 @@ <h2>3.1.4.2. Functions<a class="headerlink" href="#functions" title="Permalink t
 <h2>3.1.4.3. Analysis classes<a class="headerlink" href="#analysis-classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.analysis.rms.RMSD">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.rms.</tt><tt class="descname">RMSD</tt><big>(</big><em>traj</em>, <em>reference=None</em>, <em>select='all'</em>, <em>groupselections=None</em>, <em>filename='rmsd.dat'</em>, <em>mass_weighted=False</em>, <em>tol_mass=0.1</em>, <em>ref_frame=0</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSD"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSD" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.rms.</code><code class="descname">RMSD</code><span class="sig-paren">(</span><em>traj</em>, <em>reference=None</em>, <em>select='all'</em>, <em>groupselections=None</em>, <em>filename='rmsd.dat'</em>, <em>mass_weighted=False</em>, <em>tol_mass=0.1</em>, <em>ref_frame=0</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSD"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSD" title="Permalink to this definition">¶</a></dt>
 <dd><p>Class to perform RMSD analysis on a trajectory.</p>
-<p>Run the analysis with <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.run" title="MDAnalysis.analysis.rms.RMSD.run"><tt class="xref py py-meth docutils literal"><span class="pre">RMSD.run()</span></tt></a>, which stores the results
-in the array <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.rmsd" title="MDAnalysis.analysis.rms.RMSD.rmsd"><tt class="xref py py-attr docutils literal"><span class="pre">RMSD.rmsd</span></tt></a>:</p>
-<div class="highlight-python"><pre>frame    time (ps)    RMSD (A)</pre>
+<p>Run the analysis with <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.run" title="MDAnalysis.analysis.rms.RMSD.run"><code class="xref py py-meth docutils literal"><span class="pre">RMSD.run()</span></code></a>, which stores the results
+in the array <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.rmsd" title="MDAnalysis.analysis.rms.RMSD.rmsd"><code class="xref py py-attr docutils literal"><span class="pre">RMSD.rmsd</span></code></a>:</p>
+<div class="highlight-python"><div class="highlight"><pre>frame    time (ps)    RMSD (A)
+</pre></div>
 </div>
 <p>This class uses Douglas Theobald&#8217;s fast QCP algorithm
-<a class="reference internal" href="../lib/qcprot.html#theobald2005">[Theobald2005]</a> to calculate the RMSD.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<a class="reference internal" href="../lib/qcprot.html#theobald2005" id="id4">[Theobald2005]</a> to calculate the RMSD.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 <p>Setting up the RMSD analysis.</p>
 <p>The RMSD will be computed between <em>select</em> and <em>reference</em> for
 all frames in the trajectory in <em>universe</em>.</p>
@@ -249,41 +253,41 @@ <h2>3.1.4.3. Analysis classes<a class="headerlink" href="#analysis-classes" titl
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>traj</em></dt>
-<dd><p class="first last">universe (<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object) that contains a
+<dd><p class="first last">universe (<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object) that contains a
 trajectory</p>
 </dd>
 <dt><em>reference</em></dt>
-<dd><p class="first last">reference coordinates; <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> object; if <tt class="docutils literal"><span class="pre">None</span></tt>
-the <em>traj</em> is used (uses the current time step of the object) [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">reference coordinates; <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> object; if <code class="docutils literal"><span class="pre">None</span></code>
+the <em>traj</em> is used (uses the current time step of the object) [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>select</em></dt>
 <dd><p class="first">The selection to operate on; can be one of:</p>
 <ol class="arabic simple">
 <li>any valid selection string for
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> that produces identical
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> that produces identical
 selections in <em>mobile</em> and <em>reference</em>; or</li>
-<li>a dictionary <tt class="docutils literal"><span class="pre">{'mobile':sel1,</span> <span class="pre">'reference':sel2}</span></tt> (the
-<a class="reference internal" href="align.html#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.analysis.align.fasta2select()</span></tt></a> function returns such a
+<li>a dictionary <code class="docutils literal"><span class="pre">{'mobile':sel1,</span> <span class="pre">'reference':sel2}</span></code> (the
+<a class="reference internal" href="align.html#MDAnalysis.analysis.align.fasta2select" title="MDAnalysis.analysis.align.fasta2select"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.analysis.align.fasta2select()</span></code></a> function returns such a
 dictionary based on a <a class="reference external" href="http://www.clustal.org/">ClustalW</a> or <a class="reference external" href="http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/">STAMP</a> sequence alignment); or</li>
-<li>a tuple <tt class="docutils literal"><span class="pre">(sel1,</span> <span class="pre">sel2)</span></tt></li>
+<li>a tuple <code class="docutils literal"><span class="pre">(sel1,</span> <span class="pre">sel2)</span></code></li>
 </ol>
 <p class="last">When using 2. or 3. with <em>sel1</em> and <em>sel2</em> then these selections can also each be
 a list of selection strings (to generate a AtomGroup with defined atom order as
-described under <a class="reference internal" href="../selections.html#ordered-selections-label"><em>Ordered selections</em></a>).</p>
+described under <a class="reference internal" href="../selections.html#ordered-selections-label"><span>Ordered selections</span></a>).</p>
 </dd>
 <dt><em>groupselections</em></dt>
 <dd><p class="first">A list of selections as described for <em>select</em>. Each selection describes additional
 RMSDs to be computed <em>after the structures have be superpositioned</em> according to <em>select</em>.
-The output contains one additional column for each selection. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+The output contains one additional column for each selection. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 <div class="last admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">Experimental feature. Only limited error checking implemented.</p>
 </div>
 </dd>
 <dt><em>filename</em></dt>
-<dd><p class="first last">If set, <em>filename</em> can be used to write the results with <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.save" title="MDAnalysis.analysis.rms.RMSD.save"><tt class="xref py py-meth docutils literal"><span class="pre">RMSD.save()</span></tt></a> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">If set, <em>filename</em> can be used to write the results with <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.save" title="MDAnalysis.analysis.rms.RMSD.save"><code class="xref py py-meth docutils literal"><span class="pre">RMSD.save()</span></code></a> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>mass_weighted</em></dt>
 <dd><p class="first last">do a mass-weighted RMSD fit</p>
@@ -300,31 +304,33 @@ <h2>3.1.4.3. Analysis classes<a class="headerlink" href="#analysis-classes" titl
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span><em>groupselections</em> added</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span><em>groupselections</em> added</p>
+</div>
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.rms.RMSD.rmsd">
-<tt class="descname">rmsd</tt><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSD.rmsd" title="Permalink to this definition">¶</a></dt>
-<dd><p>Results are stored in this N×3 <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> array,
+<code class="descname">rmsd</code><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSD.rmsd" title="Permalink to this definition">¶</a></dt>
+<dd><p>Results are stored in this N×3 <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> array,
 (frame, time (ps), RMSD (Å)).</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.rms.RMSD.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSD.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSD.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSD.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSD.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Perform RMSD analysis on the trajectory.</p>
 <p>A number of parameters can be changed from the defaults. The
-result is stored as the array <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.rmsd" title="MDAnalysis.analysis.rms.RMSD.rmsd"><tt class="xref py py-attr docutils literal"><span class="pre">RMSD.rmsd</span></tt></a>.</p>
+result is stored as the array <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.rmsd" title="MDAnalysis.analysis.rms.RMSD.rmsd"><code class="xref py py-attr docutils literal"><span class="pre">RMSD.rmsd</span></code></a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>start</em>, <em>stop</em>, <em>step</em></dt>
 <dd><p class="first last">start and stop frame index with step size: analyse
-<tt class="docutils literal"><span class="pre">trajectory[start:stop:step]</span></tt> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<code class="docutils literal"><span class="pre">trajectory[start:stop:step]</span></code> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>mass_weighted</em></dt>
 <dd><p class="first last">do a mass-weighted RMSD fit</p>
@@ -345,31 +351,32 @@ <h2>3.1.4.3. Analysis classes<a class="headerlink" href="#analysis-classes" titl
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.rms.RMSD.save">
-<tt class="descname">save</tt><big>(</big><em>filename=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSD.save"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSD.save" title="Permalink to this definition">¶</a></dt>
-<dd><p>Save RMSD from <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.rmsd" title="MDAnalysis.analysis.rms.RMSD.rmsd"><tt class="xref py py-attr docutils literal"><span class="pre">RMSD.rmsd</span></tt></a> to text file <em>filename</em>.</p>
+<code class="descname">save</code><span class="sig-paren">(</span><em>filename=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSD.save"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSD.save" title="Permalink to this definition">¶</a></dt>
+<dd><p>Save RMSD from <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSD.rmsd" title="MDAnalysis.analysis.rms.RMSD.rmsd"><code class="xref py py-attr docutils literal"><span class="pre">RMSD.rmsd</span></code></a> to text file <em>filename</em>.</p>
 <p>If <em>filename</em> is not supplied then the default provided to the
 constructor is used.</p>
-<p>The data are saved with <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.savetxt.html#numpy.savetxt" title="(in NumPy v1.9)"><tt class="xref py py-func docutils literal"><span class="pre">numpy.savetxt()</span></tt></a>.</p>
+<p>The data are saved with <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.savetxt.html#numpy.savetxt" title="(in NumPy v1.9)"><code class="xref py py-func docutils literal"><span class="pre">numpy.savetxt()</span></code></a>.</p>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.rms.RMSF">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.rms.</tt><tt class="descname">RMSF</tt><big>(</big><em>atomgroup</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSF" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.rms.</code><code class="descname">RMSF</code><span class="sig-paren">(</span><em>atomgroup</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSF" title="Permalink to this definition">¶</a></dt>
 <dd><p>Class to perform RMSF analysis on a set of atoms across a trajectory.</p>
-<p>Run the analysis with <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSF.run" title="MDAnalysis.analysis.rms.RMSF.run"><tt class="xref py py-meth docutils literal"><span class="pre">RMSF.run()</span></tt></a>, which stores the results
-in the array <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSF.rmsf" title="MDAnalysis.analysis.rms.RMSF.rmsf"><tt class="xref py py-attr docutils literal"><span class="pre">RMSF.rmsf</span></tt></a>.</p>
+<p>Run the analysis with <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSF.run" title="MDAnalysis.analysis.rms.RMSF.run"><code class="xref py py-meth docutils literal"><span class="pre">RMSF.run()</span></code></a>, which stores the results
+in the array <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSF.rmsf" title="MDAnalysis.analysis.rms.RMSF.rmsf"><code class="xref py py-attr docutils literal"><span class="pre">RMSF.rmsf</span></code></a>.</p>
 <p>This class performs no coordinate transforms; RMSFs are obtained from atom
 coordinates as-is.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 <p>Calculate RMSF of given atoms across a trajectory.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>atomgroup</em></dt>
 <dd><p class="first last">AtomGroup to obtain RMSF for</p>
 </dd>
@@ -380,20 +387,20 @@ <h2>3.1.4.3. Analysis classes<a class="headerlink" href="#analysis-classes" titl
 </table>
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.rms.RMSF.rmsf">
-<tt class="descname">rmsf</tt><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSF.rmsf"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSF.rmsf" title="Permalink to this definition">¶</a></dt>
-<dd><p>Results are stored in this N-length <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> array,
+<code class="descname">rmsf</code><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSF.rmsf" title="Permalink to this definition">¶</a></dt>
+<dd><p>Results are stored in this N-length <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> array,
 giving RMSFs for each of the given atoms.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt>
-<tt class="descname">rmsf</tt><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSF.rmsf"><span class="viewcode-link">[source]</span></a></dt>
-<dd><p>RMSF data; only available after using <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSF.run" title="MDAnalysis.analysis.rms.RMSF.run"><tt class="xref py py-meth docutils literal"><span class="pre">RMSF.run()</span></tt></a></p>
+<code class="descname">rmsf</code></dt>
+<dd><p>RMSF data; only available after using <a class="reference internal" href="#MDAnalysis.analysis.rms.RMSF.run" title="MDAnalysis.analysis.rms.RMSF.run"><code class="xref py py-meth docutils literal"><span class="pre">RMSF.run()</span></code></a></p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.rms.RMSF.run">
-<tt class="descname">run</tt><big>(</big><em>start=0</em>, <em>stop=-1</em>, <em>step=1</em>, <em>progout=10</em>, <em>quiet=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSF.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSF.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>start=0</em>, <em>stop=-1</em>, <em>step=1</em>, <em>progout=10</em>, <em>quiet=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/rms.html#RMSF.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.rms.RMSF.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate RMSF of given atoms across a trajectory.</p>
 <p>This method implements an algorithm for computing sums of squares while
 avoiding overflows and underflows; please reference:</p>
@@ -409,7 +416,7 @@ <h2>3.1.4.3. Analysis classes<a class="headerlink" href="#analysis-classes" titl
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>start</em></dt>
 <dd><p class="first last">starting frame [0]</p>
 </dd>
@@ -421,11 +428,11 @@ <h2>3.1.4.3. Analysis classes<a class="headerlink" href="#analysis-classes" titl
 </dd>
 <dt><em>progout</em></dt>
 <dd><p class="first last">number of frames to iterate through between updates to progress
-output; <tt class="docutils literal"><span class="pre">None</span></tt> for no updates [10]</p>
+output; <code class="docutils literal"><span class="pre">None</span></code> for no updates [10]</p>
 </dd>
 <dt><em>quiet</em></dt>
-<dd><p class="first last">if <tt class="docutils literal"><span class="pre">True</span></tt>, suppress all output (implies <em>progout</em> = <tt class="docutils literal"><span class="pre">None</span></tt>)
-[<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">if <code class="docutils literal"><span class="pre">True</span></code>, suppress all output (implies <em>progout</em> = <code class="docutils literal"><span class="pre">None</span></code>)
+[<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -445,7 +452,7 @@ <h2>3.1.4.3. Analysis classes<a class="headerlink" href="#analysis-classes" titl
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
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         <li class="right" style="margin-right: 10px">
@@ -460,11 +467,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="distances.html" title="3.1.3. Distance analysis — MDAnalysis.analysis.distances"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -474,7 +481,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/waterdynamics.html b/package/doc/html/documentation_pages/analysis/waterdynamics.html
index 70477caccd4..a6e43286796 100644
--- a/package/doc/html/documentation_pages/analysis/waterdynamics.html
+++ b/package/doc/html/documentation_pages/analysis/waterdynamics.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3.6.2. Water dynamics analysis — MDAnalysis.analysis.waterdynamics &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3.6.2. Water dynamics analysis — MDAnalysis.analysis.waterdynamics &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
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@@ -16,7 +14,7 @@
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       var DOCUMENTATION_OPTIONS = {
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-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="3. Analysis modules" href="../analysis_modules.html" />
     <link rel="next" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="prev" title="3.6.1. Generating densities from trajectories — MDAnalysis.analysis.density" href="density.html" /> 
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
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@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="density.html" title="3.6.1. Generating densities from trajectories — MDAnalysis.analysis.density"
              accesskey="P">previous</a> |</li>
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-          <li><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" accesskey="U">3. Analysis modules</a> &raquo;</li> 
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.6.2. Water dynamics analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.6.2. Water dynamics analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></code></a><ul>
 <li><a class="reference internal" href="#examples">3.6.2.1. Examples</a><ul>
 <li><a class="reference internal" href="#hydrogenbondlifetimes">3.6.2.1.1. HydrogenBondLifetimes</a></li>
 <li><a class="reference internal" href="#waterorientationalrelaxation">3.6.2.1.2. WaterOrientationalRelaxation</a></li>
@@ -86,16 +84,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="density.html"
-                        title="previous chapter">3.6.1. Generating densities from trajectories &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.analysis.density</span></tt></a></p>
+                        title="previous chapter">3.6.1. Generating densities from trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.density</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="../topology_modules.html"
                         title="next chapter">4. Topology modules</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/analysis/waterdynamics.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
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   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -114,10 +114,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.analysis.waterdynamics"></span><div class="section" id="water-dynamics-analysis-mdanalysis-analysis-waterdynamics">
-<h1>3.6.2. Water dynamics analysis &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.waterdynamics" title="MDAnalysis.analysis.waterdynamics"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></tt></a><a class="headerlink" href="#water-dynamics-analysis-mdanalysis-analysis-waterdynamics" title="Permalink to this headline">¶</a></h1>
+<h1>3.6.2. Water dynamics analysis &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.waterdynamics" title="MDAnalysis.analysis.waterdynamics"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></code></a><a class="headerlink" href="#water-dynamics-analysis-mdanalysis-analysis-waterdynamics" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -130,12 +130,13 @@ <h1>3.6.2. Water dynamics analysis &#8212; <a class="reference internal" href="#
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 <p>This module provides functions to analize water dynamics trajectories and water interactions with other molecules.
-The functions in this module are: water orientational relaxation (WOR) <a class="reference internal" href="#yeh1999">[Yeh1999]</a>, hydrogen bond lifetimes (HBL) <a class="reference internal" href="#rapaport1983">[Rapaport1983]</a>,
-angular distribution (AD) <a class="reference internal" href="#grigera1995">[Grigera1995]</a>, mean square displacement (MSD) <a class="reference internal" href="#brodka1994">[Brodka1994]</a> and survival probability (SP) <a class="reference internal" href="#liu2004">[Liu2004]</a>.</p>
-<p>For more information about this type of analysis please refer to <a class="reference internal" href="#araya-secchi2014">[Araya-Secchi2014]</a> (water in a protein cavity) and <a class="reference internal" href="#milischuk2011">[Milischuk2011]</a> (water in a nanopore).</p>
+The functions in this module are: water orientational relaxation (WOR) <a class="reference internal" href="#yeh1999" id="id1">[Yeh1999]</a>, hydrogen bond lifetimes (HBL) <a class="reference internal" href="#rapaport1983" id="id2">[Rapaport1983]</a>,
+angular distribution (AD) <a class="reference internal" href="#grigera1995" id="id3">[Grigera1995]</a>, mean square displacement (MSD) <a class="reference internal" href="#brodka1994" id="id4">[Brodka1994]</a> and survival probability (SP) <a class="reference internal" href="#liu2004" id="id5">[Liu2004]</a>.</p>
+<p>For more information about this type of analysis please refer to <a class="reference internal" href="#araya-secchi2014" id="id6">[Araya-Secchi2014]</a> (water in a protein cavity) and <a class="reference internal" href="#milischuk2011" id="id7">[Milischuk2011]</a> (water in a nanopore).</p>
 <p class="rubric">References</p>
 <table class="docutils citation" frame="void" id="rapaport1983" rules="none">
 <colgroup><col class="label" /><col /></colgroup>
@@ -192,7 +193,7 @@ <h1>3.6.2. Water dynamics analysis &#8212; <a class="reference internal" href="#
 <h2>3.6.2.1. Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
 <div class="section" id="hydrogenbondlifetimes">
 <h3>3.6.2.1.1. HydrogenBondLifetimes<a class="headerlink" href="#hydrogenbondlifetimes" title="Permalink to this headline">¶</a></h3>
-<p>Analyzing hydrogen bond lifetimes (HBL) <a class="reference internal" href="#MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes" title="MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes"><tt class="xref py py-class docutils literal"><span class="pre">HydrogenBondLifetimes</span></tt></a>, both continuos and intermittent. In this case we are analyzing
+<p>Analyzing hydrogen bond lifetimes (HBL) <a class="reference internal" href="#MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes" title="MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes"><code class="xref py py-class docutils literal"><span class="pre">HydrogenBondLifetimes</span></code></a>, both continuos and intermittent. In this case we are analyzing
 how residue 38 interact with a water sphere of radius 6.0 centered on the geometric center of protein and
 residue 42. If the hydrogen bond lifetimes are very stable, we can assume that residue 38 is hydrophilic, on the other
 hand, if the  are very unstable, we can assume that residue 38 is hydrophobic:</p>
@@ -218,7 +219,7 @@ <h3>3.6.2.1.1. HydrogenBondLifetimes<a class="headerlink" href="#hydrogenbondlif
 </div>
 <div class="section" id="waterorientationalrelaxation">
 <h3>3.6.2.1.2. WaterOrientationalRelaxation<a class="headerlink" href="#waterorientationalrelaxation" title="Permalink to this headline">¶</a></h3>
-<p>Analyzing water orientational relaxation (WOR) <a class="reference internal" href="#MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation" title="MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation"><tt class="xref py py-class docutils literal"><span class="pre">WaterOrientationalRelaxation</span></tt></a>. In this case we are analyzing &#8220;how fast&#8221; water molecules are rotating/changing direction. If WOR is very stable we can assume that water molecules are rotating/changing direction very slow, on the other hand, if WOR decay very fast, we can assume that water molecules are rotating/changing direction very fast:</p>
+<p>Analyzing water orientational relaxation (WOR) <a class="reference internal" href="#MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation" title="MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation"><code class="xref py py-class docutils literal"><span class="pre">WaterOrientationalRelaxation</span></code></a>. In this case we are analyzing &#8220;how fast&#8221; water molecules are rotating/changing direction. If WOR is very stable we can assume that water molecules are rotating/changing direction very slow, on the other hand, if WOR decay very fast, we can assume that water molecules are rotating/changing direction very fast:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">MDAnalysis</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis.analysis.waterdynamics</span> <span class="kn">import</span> <span class="n">WaterOrientationalRelaxation</span> <span class="k">as</span> <span class="n">WOR</span>
 
@@ -239,7 +240,7 @@ <h3>3.6.2.1.2. WaterOrientationalRelaxation<a class="headerlink" href="#waterori
 </div>
 <div class="section" id="angulardistribution">
 <h3>3.6.2.1.3. AngularDistribution<a class="headerlink" href="#angulardistribution" title="Permalink to this headline">¶</a></h3>
-<p>Analyzing angular distribution (AD) <a class="reference internal" href="#MDAnalysis.analysis.waterdynamics.AngularDistribution" title="MDAnalysis.analysis.waterdynamics.AngularDistribution"><tt class="xref py py-class docutils literal"><span class="pre">AngularDistribution</span></tt></a> for OH vector, HH vector and dipole vector. It returns
+<p>Analyzing angular distribution (AD) <a class="reference internal" href="#MDAnalysis.analysis.waterdynamics.AngularDistribution" title="MDAnalysis.analysis.waterdynamics.AngularDistribution"><code class="xref py py-class docutils literal"><span class="pre">AngularDistribution</span></code></a> for OH vector, HH vector and dipole vector. It returns
 a line histogram with vector orientation preference. A straight line in the output graphic means no preferential
 orientation in water molecules. In this case we are analyzing if water molecules have some orientational
 preference, in this way we can see if water molecules are under an electric field or if they are interacting
@@ -284,7 +285,7 @@ <h3>3.6.2.1.4. MeanSquareDisplacement<a class="headerlink" href="#meansquaredisp
 </div>
 <div class="section" id="survivalprobability">
 <h3>3.6.2.1.5. SurvivalProbability<a class="headerlink" href="#survivalprobability" title="Permalink to this headline">¶</a></h3>
-<p>Analyzing survival probability (SP) <a class="reference internal" href="#MDAnalysis.analysis.waterdynamics.SurvivalProbability" title="MDAnalysis.analysis.waterdynamics.SurvivalProbability"><tt class="xref py py-class docutils literal"><span class="pre">SurvivalProbability</span></tt></a> for water molecules. In this case we are analyzing how long water
+<p>Analyzing survival probability (SP) <a class="reference internal" href="#MDAnalysis.analysis.waterdynamics.SurvivalProbability" title="MDAnalysis.analysis.waterdynamics.SurvivalProbability"><code class="xref py py-class docutils literal"><span class="pre">SurvivalProbability</span></code></a> for water molecules. In this case we are analyzing how long water
 molecules remain in a sphere of radius 12.3 centered in the geometrical center of resid 42, 26, 34 and 80.
 A slow decay of SP means a long permanence time of water molecules in the zone, on the
 other hand, a fast decay means a short permanence time:</p>
@@ -310,8 +311,8 @@ <h2>3.6.2.2. Output<a class="headerlink" href="#output" title="Permalink to this
 <div class="section" id="id8">
 <h3>3.6.2.2.1. HydrogenBondLifetimes<a class="headerlink" href="#id8" title="Permalink to this headline">¶</a></h3>
 <p>Hydrogen bond lifetimes (HBL) data is returned per window timestep, which is stored in
-<tt class="xref py py-attr docutils literal"><span class="pre">HydrogenBondLifetimes.timeseries</span></tt> (in all the following descriptions, # indicates comments that are not part of the output):</p>
-<div class="highlight-python"><pre>results = [
+<code class="xref py py-attr docutils literal"><span class="pre">HydrogenBondLifetimes.timeseries</span></code> (in all the following descriptions, # indicates comments that are not part of the output):</p>
+<div class="highlight-python"><div class="highlight"><pre>results = [
     [ # time t0
         &lt;HBL_c&gt;, &lt;HBL_i&gt;
     ],
@@ -319,14 +320,15 @@ <h3>3.6.2.2.1. HydrogenBondLifetimes<a class="headerlink" href="#id8" title="Per
         &lt;HBL_c&gt;, &lt;HBL_i&gt;
     ],
     ...
- ]</pre>
+ ]
+</pre></div>
 </div>
 </div>
 <div class="section" id="id9">
 <h3>3.6.2.2.2. WaterOrientationalRelaxation<a class="headerlink" href="#id9" title="Permalink to this headline">¶</a></h3>
 <p>Water orientational relaxation (WOR) data is returned per window timestep, which is stored in
-<tt class="xref py py-attr docutils literal"><span class="pre">WaterOrientationalRelaxation.timeseries</span></tt>:</p>
-<div class="highlight-python"><pre>results = [
+<code class="xref py py-attr docutils literal"><span class="pre">WaterOrientationalRelaxation.timeseries</span></code>:</p>
+<div class="highlight-python"><div class="highlight"><pre>results = [
     [ # time t0
         &lt;WOR_OH&gt;, &lt;WOR_HH&gt;, &lt;WOR_dip&gt;
     ],
@@ -334,14 +336,15 @@ <h3>3.6.2.2.2. WaterOrientationalRelaxation<a class="headerlink" href="#id9" tit
         &lt;WOR_OH&gt;, &lt;WOR_HH&gt;, &lt;WOR_dip&gt;
     ],
     ...
- ]</pre>
+ ]
+</pre></div>
 </div>
 </div>
 <div class="section" id="id10">
 <h3>3.6.2.2.3. AngularDistribution<a class="headerlink" href="#id10" title="Permalink to this headline">¶</a></h3>
 <p>Angular distribution (AD) data is returned per vector, which is stored in
-<tt class="xref py py-attr docutils literal"><span class="pre">AngularDistribution.graph</span></tt>. In fact, AngularDistribution returns a histogram:</p>
-<div class="highlight-python"><pre>results = [
+<code class="xref py py-attr docutils literal"><span class="pre">AngularDistribution.graph</span></code>. In fact, AngularDistribution returns a histogram:</p>
+<div class="highlight-python"><div class="highlight"><pre>results = [
     [ # OH vector values
       # the values are order in this way: &lt;x_axis  y_axis&gt;
         &lt;cos_theta0 ang_distr0&gt;, &lt;cos_theta1 ang_distr1&gt;, ...
@@ -352,27 +355,30 @@ <h3>3.6.2.2.3. AngularDistribution<a class="headerlink" href="#id10" title="Perm
     [ # dip vector values
        &lt;cos_theta0 ang_distr0&gt;, &lt;cos_theta1 ang_distr1&gt;, ...
     ],
- ]</pre>
+ ]
+</pre></div>
 </div>
 </div>
 <div class="section" id="id11">
 <h3>3.6.2.2.4. MeanSquareDisplacement<a class="headerlink" href="#id11" title="Permalink to this headline">¶</a></h3>
 <p>Mean Square Displacement (MSD) data is returned in a list, which each element represents a MSD value in its respective
-window timestep. Data is stored in <tt class="xref py py-attr docutils literal"><span class="pre">MeanSquareDisplacement.timeseries</span></tt>:</p>
-<div class="highlight-python"><pre>results = [
+window timestep. Data is stored in <code class="xref py py-attr docutils literal"><span class="pre">MeanSquareDisplacement.timeseries</span></code>:</p>
+<div class="highlight-python"><div class="highlight"><pre>results = [
      #MSD values orders by window timestep
         &lt;MSD_t0&gt;, &lt;MSD_t1&gt;, ...
- ]</pre>
+ ]
+</pre></div>
 </div>
 </div>
 <div class="section" id="id12">
 <h3>3.6.2.2.5. SurvivalProbability<a class="headerlink" href="#id12" title="Permalink to this headline">¶</a></h3>
 <p>Survival Probability (SP) data is returned in a list, which each element represents a SP value in its respective
-window timestep. Data is stored in <tt class="xref py py-attr docutils literal"><span class="pre">SurvivalProbability.timeseries</span></tt>:</p>
-<div class="highlight-python"><pre>results = [
+window timestep. Data is stored in <code class="xref py py-attr docutils literal"><span class="pre">SurvivalProbability.timeseries</span></code>:</p>
+<div class="highlight-python"><div class="highlight"><pre>results = [
      # SP values order by window timestep
         &lt;SP_t0&gt;, &lt;SP_t1&gt;, ...
- ]</pre>
+ ]
+</pre></div>
 </div>
 </div>
 </div>
@@ -380,8 +386,8 @@ <h3>3.6.2.2.5. SurvivalProbability<a class="headerlink" href="#id12" title="Perm
 <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.waterdynamics.</tt><tt class="descname">HydrogenBondLifetimes</tt><big>(</big><em>universe</em>, <em>selection1</em>, <em>selection2</em>, <em>t0</em>, <em>tf</em>, <em>dtmax</em>, <em>nproc=1</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#HydrogenBondLifetimes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes" title="Permalink to this definition">¶</a></dt>
-<dd><p>This is a autocorrelation function that gives the &#8220;Hydrogen Bond Lifetimes&#8221; (HBL) proposed by D.C. Rapaport <a class="reference internal" href="#rapaport1983">[Rapaport1983]</a>. From this
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.waterdynamics.</code><code class="descname">HydrogenBondLifetimes</code><span class="sig-paren">(</span><em>universe</em>, <em>selection1</em>, <em>selection2</em>, <em>t0</em>, <em>tf</em>, <em>dtmax</em>, <em>nproc=1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#HydrogenBondLifetimes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes" title="Permalink to this definition">¶</a></dt>
+<dd><p>This is a autocorrelation function that gives the &#8220;Hydrogen Bond Lifetimes&#8221; (HBL) proposed by D.C. Rapaport <a class="reference internal" href="#rapaport1983" id="id13">[Rapaport1983]</a>. From this
 function we can obtain the continuos and intermittent behavior of hydrogen bonds in time. A
 fast decay in these parameters indicate a fast change in HBs connectivity. A slow decay
 indicate very stables hydrogen bonds, like in ice. The HBL is also know as &#8220;Hydrogen Bond Population
@@ -395,13 +401,14 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 \[C_{HB}^i(\tau) = \frac{\sum_{ij}h_{ij}(t_0)h_{ij}(t_0+\tau)}{\sum_{ij}h_{ij}(t_0)}\]</div>
 <p>where <span class="math">\(h_{ij}(t_0+\tau)=1\)</span> if there is a H-bond between a pair <span class="math">\(ij\)</span> at time
 <span class="math">\(t_0+\tau\)</span> (intermittent) and <span class="math">\(h_{ij}(t_0+\tau)=0\)</span> otherwise.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Universe object</p>
 </dd>
@@ -431,7 +438,7 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </table>
 <dl class="method">
 <dt id="MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#HydrogenBondLifetimes.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#HydrogenBondLifetimes.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Analyze trajectory and produce timeseries</p>
 </dd></dl>
 
@@ -439,7 +446,7 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.waterdynamics.</tt><tt class="descname">WaterOrientationalRelaxation</tt><big>(</big><em>universe</em>, <em>selection</em>, <em>t0</em>, <em>tf</em>, <em>dtmax</em>, <em>nproc=1</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#WaterOrientationalRelaxation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.waterdynamics.</code><code class="descname">WaterOrientationalRelaxation</code><span class="sig-paren">(</span><em>universe</em>, <em>selection</em>, <em>t0</em>, <em>tf</em>, <em>dtmax</em>, <em>nproc=1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#WaterOrientationalRelaxation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation" title="Permalink to this definition">¶</a></dt>
 <dd><p>Function to evaluate the Water Orientational Relaxation proposed by Yu-ling Yeh
 and Chung-Yuan Mou [<a class="reference internal" href="#yeh1999">Yeh1999</a>]. WaterOrientationalRelaxation indicates &#8220;how fast&#8221; water molecules are rotating
 or changing direction. This is a time correlation function given by:</p>
@@ -447,13 +454,14 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 \[C_{\hat u}(\tau)=\langle \mathit{P}_2[\mathbf{\hat{u}}(t_0)\cdot\mathbf{\hat{u}}(t_0+\tau)]\rangle\]</div>
 <p>where <span class="math">\(P_2=(3x^2-1)/2\)</span> is the second-order Legendre polynomial and <span class="math">\(\hat{u}\)</span> is
 a unit vector along HH, OH or dipole vector.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Universe object</p>
 </dd>
@@ -476,7 +484,7 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </table>
 <dl class="method">
 <dt id="MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#WaterOrientationalRelaxation.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#WaterOrientationalRelaxation.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Analyze trajectory and produce timeseries</p>
 </dd></dl>
 
@@ -484,19 +492,20 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.waterdynamics.AngularDistribution">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.waterdynamics.</tt><tt class="descname">AngularDistribution</tt><big>(</big><em>universe</em>, <em>selection_str</em>, <em>bins=40</em>, <em>nproc=1</em>, <em>axis='z'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#AngularDistribution"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.AngularDistribution" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.waterdynamics.</code><code class="descname">AngularDistribution</code><span class="sig-paren">(</span><em>universe</em>, <em>selection_str</em>, <em>bins=40</em>, <em>nproc=1</em>, <em>axis='z'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#AngularDistribution"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.AngularDistribution" title="Permalink to this definition">¶</a></dt>
 <dd><p>The angular distribution function (AD) is defined as the distribution
 probability of the cosine of the <span class="math">\(\theta\)</span> angle formed by the OH vector, HH vector
 or dipolar vector of water molecules and a vector <span class="math">\(\hat n\)</span> parallel to chosen axis
 (z is the default value). The cosine is define as <span class="math">\(\cos \theta = \hat u \cdot \hat n\)</span>, where <span class="math">\(\hat u\)</span> is OH, HH or dipole vector.
 It creates a histogram and returns a list of lists, see <a class="reference internal" href="#output">Output</a>. The AD is also know as Angular Probability (AP).</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Universe object</p>
 </dd>
@@ -517,7 +526,7 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </table>
 <dl class="method">
 <dt id="MDAnalysis.analysis.waterdynamics.AngularDistribution.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#AngularDistribution.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.AngularDistribution.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#AngularDistribution.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.AngularDistribution.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Function to evaluate the angular distribution of cos(theta)</p>
 </dd></dl>
 
@@ -525,7 +534,7 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.waterdynamics.</tt><tt class="descname">MeanSquareDisplacement</tt><big>(</big><em>universe</em>, <em>selection</em>, <em>t0</em>, <em>tf</em>, <em>dtmax</em>, <em>nproc=1</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#MeanSquareDisplacement"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.waterdynamics.</code><code class="descname">MeanSquareDisplacement</code><span class="sig-paren">(</span><em>universe</em>, <em>selection</em>, <em>t0</em>, <em>tf</em>, <em>dtmax</em>, <em>nproc=1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#MeanSquareDisplacement"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement" title="Permalink to this definition">¶</a></dt>
 <dd><p>Function to evaluate the Mean Square Displacement (<a class="reference external" href="http://en.wikipedia.org/wiki/Mean_squared_displacement">MSD</a>). The MSD gives the average distance that
 particles travels. The MSD is given by:</p>
 <div class="math">
@@ -533,13 +542,14 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 <p>where <span class="math">\(r(t)\)</span> is the position of particle in time <span class="math">\(t\)</span>, <span class="math">\(\Delta r(t)\)</span> is the displacement
 after time lag <span class="math">\(t\)</span>, <span class="math">\(n\)</span> is the dimensionality, in this case <span class="math">\(n=3\)</span>, <span class="math">\(D\)</span> is the diffusion
 coefficient and <span class="math">\(t\)</span> is the time.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Universe object</p>
 </dd>
@@ -562,7 +572,7 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </table>
 <dl class="method">
 <dt id="MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#MeanSquareDisplacement.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#MeanSquareDisplacement.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Analyze trajectory and produce timeseries</p>
 </dd></dl>
 
@@ -570,20 +580,21 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.waterdynamics.SurvivalProbability">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.waterdynamics.</tt><tt class="descname">SurvivalProbability</tt><big>(</big><em>universe</em>, <em>selection</em>, <em>t0</em>, <em>tf</em>, <em>dtmax</em>, <em>nproc=1</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#SurvivalProbability"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.SurvivalProbability" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.waterdynamics.</code><code class="descname">SurvivalProbability</code><span class="sig-paren">(</span><em>universe</em>, <em>selection</em>, <em>t0</em>, <em>tf</em>, <em>dtmax</em>, <em>nproc=1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#SurvivalProbability"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.SurvivalProbability" title="Permalink to this definition">¶</a></dt>
 <dd><p>Function to evaluate the Survival Probability (SP). The SP gives the probability
 for a group of particles to remain in certain region. The SP is given by:</p>
 <div class="math">
 \[P(\tau) = \frac1T \sum_{t=1}^T \frac{N(t,t+\tau)}{N(t)}\]</div>
 <p>where <span class="math">\(T\)</span> is the maximum time of simulation, <span class="math">\(\tau\)</span> is the timestep and
 <span class="math">\(N\)</span> the number of particles in certain time.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Universe object</p>
 </dd>
@@ -607,7 +618,7 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </table>
 <dl class="method">
 <dt id="MDAnalysis.analysis.waterdynamics.SurvivalProbability.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#SurvivalProbability.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.SurvivalProbability.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/waterdynamics.html#SurvivalProbability.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.waterdynamics.SurvivalProbability.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Analyze trajectory and produce timeseries</p>
 </dd></dl>
 
@@ -622,7 +633,7 @@ <h2>3.6.2.3. Classes<a class="headerlink" href="#classes" title="Permalink to th
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -637,11 +648,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="density.html" title="3.6.1. Generating densities from trajectories — MDAnalysis.analysis.density"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
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-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -651,7 +662,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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diff --git a/package/doc/html/documentation_pages/analysis/x3dna.html b/package/doc/html/documentation_pages/analysis/x3dna.html
index c30cd0f270a..585bfbaaa8e 100644
--- a/package/doc/html/documentation_pages/analysis/x3dna.html
+++ b/package/doc/html/documentation_pages/analysis/x3dna.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
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+    <title>3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles — MDAnalysis.analysis.x3dna &mdash; MDAnalysis 0.11.0 documentation</title>
     
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   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.x3dna</span></tt></a><ul>
+<li><a class="reference internal" href="#">3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.x3dna</span></code></a><ul>
 <li><a class="reference internal" href="#examples">3.4.2.1. Examples</a><ul>
 <li><a class="reference internal" href="#single-structure">3.4.2.1.1. Single structure</a></li>
 <li><a class="reference internal" href="#trajectory">3.4.2.1.2. Trajectory</a></li>
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   <span class="target" id="module-MDAnalysis.analysis.x3dna"></span><div class="section" id="generation-and-analysis-of-x3dna-helicoidal-parameter-profiles-mdanalysis-analysis-x3dna">
-<h1>3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.x3dna" title="MDAnalysis.analysis.x3dna"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.x3dna</span></tt></a><a class="headerlink" href="#generation-and-analysis-of-x3dna-helicoidal-parameter-profiles-mdanalysis-analysis-x3dna" title="Permalink to this headline">¶</a></h1>
+<h1>3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212; <a class="reference internal" href="#module-MDAnalysis.analysis.x3dna" title="MDAnalysis.analysis.x3dna"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.x3dna</span></code></a><a class="headerlink" href="#generation-and-analysis-of-x3dna-helicoidal-parameter-profiles-mdanalysis-analysis-x3dna" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -121,7 +121,7 @@ <h1>3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212
 </tbody>
 </table>
 <p>With the help of this module, <a class="reference external" href="http://x3dna.org/">X3DNA</a> can be run on frames in a trajectory. Data
-can be combined and analyzed. <a class="reference external" href="http://x3dna.org/">X3DNA</a> <a class="reference internal" href="#lu2003">[Lu2003]</a> <a class="reference internal" href="#lu2008">[Lu2008]</a> must be installed
+can be combined and analyzed. <a class="reference external" href="http://x3dna.org/">X3DNA</a> <a class="reference internal" href="#lu2003" id="id1">[Lu2003]</a> <a class="reference internal" href="#lu2008" id="id2">[Lu2008]</a> must be installed
 separately.</p>
 <p class="rubric">References</p>
 <table class="docutils citation" frame="void" id="lu2003" rules="none">
@@ -168,8 +168,8 @@ <h3>3.4.2.1.2. Trajectory<a class="headerlink" href="#trajectory" title="Permali
 <span class="n">H</span><span class="o">.</span><span class="n">save</span><span class="p">()</span>
 </pre></div>
 </div>
-<p>The profiles are available as the attribute <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.profiles" title="MDAnalysis.analysis.x3dna.X3DNAtraj.profiles"><tt class="xref py py-attr docutils literal"><span class="pre">X3DNAtraj.profiles</span></tt></a>
-(<tt class="docutils literal"><span class="pre">H.profiles</span></tt> in the example) and are indexed by frame number but
+<p>The profiles are available as the attribute <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.profiles" title="MDAnalysis.analysis.x3dna.X3DNAtraj.profiles"><code class="xref py py-attr docutils literal"><span class="pre">X3DNAtraj.profiles</span></code></a>
+(<code class="docutils literal"><span class="pre">H.profiles</span></code> in the example) and are indexed by frame number but
 can also be indexed by an arbitrary order parameter as shown in the
 next example.</p>
 </div>
@@ -178,28 +178,29 @@ <h3>3.4.2.1.2. Trajectory<a class="headerlink" href="#trajectory" title="Permali
 <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.analysis.x3dna.X3DNA">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.x3dna.</tt><tt class="descname">X3DNA</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNA"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.x3dna.</code><code class="descname">X3DNA</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNA"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA" title="Permalink to this definition">¶</a></dt>
 <dd><p>Run <a class="reference external" href="http://x3dna.org/">X3DNA</a> on a single frame or a DCD trajectory.</p>
 <p>Only a subset of all X3DNA control parameters is supported and can be set
 with keyword arguments. For further details on <a class="reference external" href="http://x3dna.org/">X3DNA</a> see the <a class="reference external" href="http://forum.x3dna.org/">X3DNA docs</a>.</p>
-<p>Running X3DNA with the <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA" title="MDAnalysis.analysis.x3dna.X3DNA"><tt class="xref py py-class docutils literal"><span class="pre">X3DNA</span></tt></a> class is a 3-step process:</p>
+<p>Running X3DNA with the <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA" title="MDAnalysis.analysis.x3dna.X3DNA"><code class="xref py py-class docutils literal"><span class="pre">X3DNA</span></code></a> class is a 3-step process:</p>
 <blockquote>
 <div><ol class="arabic simple">
 <li>set up the class with all desired parameters</li>
-<li>run X3DNA with <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.run" title="MDAnalysis.analysis.x3dna.X3DNA.run"><tt class="xref py py-meth docutils literal"><span class="pre">X3DNA.run()</span></tt></a></li>
-<li>collect the data from the output file with <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.collect" title="MDAnalysis.analysis.x3dna.X3DNA.collect"><tt class="xref py py-meth docutils literal"><span class="pre">X3DNA.collect()</span></tt></a></li>
+<li>run X3DNA with <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.run" title="MDAnalysis.analysis.x3dna.X3DNA.run"><code class="xref py py-meth docutils literal"><span class="pre">X3DNA.run()</span></code></a></li>
+<li>collect the data from the output file with <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.collect" title="MDAnalysis.analysis.x3dna.X3DNA.collect"><code class="xref py py-meth docutils literal"><span class="pre">X3DNA.collect()</span></code></a></li>
 </ol>
 </div></blockquote>
 <p>The class also provides some simple plotting functions of the collected
-data such as <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.plot" title="MDAnalysis.analysis.x3dna.X3DNA.plot"><tt class="xref py py-meth docutils literal"><span class="pre">X3DNA.plot()</span></tt></a> or <tt class="xref py py-meth docutils literal"><span class="pre">X3DNA.plot3D()</span></tt>.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+data such as <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.plot" title="MDAnalysis.analysis.x3dna.X3DNA.plot"><code class="xref py py-meth docutils literal"><span class="pre">X3DNA.plot()</span></code></a> or <code class="xref py py-meth docutils literal"><span class="pre">X3DNA.plot3D()</span></code>.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
 <p>Set up parameters to run <a class="reference external" href="http://x3dna.org/">X3DNA</a> on PDB <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><p class="first"><em>filename</em></p>
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><p class="first"><em>filename</em></p>
 <blockquote>
 <div><p>The <em>filename</em> is used as input for X3DNA in the &#8220;xdna_ensemble&#8221;
 command.  It specifies the name of a PDB coordinate file
@@ -211,10 +212,10 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 </div></blockquote>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><p class="first"><em>executable</em></p>
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><p class="first"><em>executable</em></p>
 <blockquote>
 <div><p>Path to the <strong class="program">xdna_ensemble</strong> executable directories
-(e.g. <tt class="docutils literal"><span class="pre">/opt/x3dna/2.1</span> <span class="pre">and</span> <span class="pre">/opt/x3dna/2.1/bin</span></tt>) must be set
+(e.g. <code class="docutils literal"><span class="pre">/opt/x3dna/2.1</span> <span class="pre">and</span> <span class="pre">/opt/x3dna/2.1/bin</span></code>) must be set
 and then added to export in bashrc file. See X3DNA
 documentation for set-up instructions.</p>
 </div></blockquote>
@@ -231,35 +232,35 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 </table>
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.x3dna.X3DNA.profiles">
-<tt class="descname">profiles</tt><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p><tt class="docutils literal"><span class="pre">x3dna_ensemble</span> <span class="pre">analyze</span> <span class="pre">-b</span> <span class="pre">355d.bps</span> <span class="pre">-p</span> <span class="pre">pdbfile</span> <span class="pre">attribute</span></tt>:
-After running <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.collect" title="MDAnalysis.analysis.x3dna.X3DNA.collect"><tt class="xref py py-meth docutils literal"><span class="pre">X3DNA.collect()</span></tt></a>, this dict contains all the
+<code class="descname">profiles</code><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.profiles" title="Permalink to this definition">¶</a></dt>
+<dd><p><code class="docutils literal"><span class="pre">x3dna_ensemble</span> <span class="pre">analyze</span> <span class="pre">-b</span> <span class="pre">355d.bps</span> <span class="pre">-p</span> <span class="pre">pdbfile</span> <span class="pre">attribute</span></code>:
+After running <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.collect" title="MDAnalysis.analysis.x3dna.X3DNA.collect"><code class="xref py py-meth docutils literal"><span class="pre">X3DNA.collect()</span></code></a>, this dict contains all the
 X3DNA profiles, indexed by the frame number. If only a single
-frame was analyzed then this will be <tt class="docutils literal"><span class="pre">X3DNA.profiles[0]</span></tt>. Note
+frame was analyzed then this will be <code class="docutils literal"><span class="pre">X3DNA.profiles[0]</span></code>. Note
 that the order is random; one needs to sort the keys first.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNA.collect">
-<tt class="descname">collect</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNA.collect"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.collect" title="Permalink to this definition">¶</a></dt>
+<code class="descname">collect</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNA.collect"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.collect" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse the output from a X3DNA run into numpy recarrays.</p>
 <p>Can deal with outputs containing multiple frames. Output format:</p>
-<p>The method saves the result as <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.profiles" title="MDAnalysis.analysis.x3dna.X3DNA.profiles"><tt class="xref py py-attr docutils literal"><span class="pre">X3DNA.profiles</span></tt></a>, a dictionary
+<p>The method saves the result as <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.profiles" title="MDAnalysis.analysis.x3dna.X3DNA.profiles"><code class="xref py py-attr docutils literal"><span class="pre">X3DNA.profiles</span></code></a>, a dictionary
 indexed by the frame number. Each entry is a
-<tt class="xref py py-class docutils literal"><span class="pre">np.recarray</span></tt>.</p>
+<code class="xref py py-class docutils literal"><span class="pre">np.recarray</span></code>.</p>
 <p>If the keyword <em>outdir</em> is supplied (e.g. &#8221;.&#8221;) then each profile is
 saved to a gzipped data file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>run</em></dt>
 <dd><p class="first last">identifier, free form [1]</p>
 </dd>
 <dt><em>outdir</em></dt>
 <dd><p class="first last">save output data under <em>outdir</em>/<em>run</em> if set to any other
-value but <tt class="docutils literal"><span class="pre">None</span></tt> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+value but <code class="docutils literal"><span class="pre">None</span></code> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -270,28 +271,30 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNA.mean">
-<tt class="descname">mean</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.mean" title="Permalink to this definition">¶</a></dt>
+<code class="descname">mean</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.mean" title="Permalink to this definition">¶</a></dt>
 <dd><p>H.mean() returns the mean value for the base parameters (order of base parameters:Shear,Stretch,Stagger,
 Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNA.mean_std">
-<tt class="descname">mean_std</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.mean_std" title="Permalink to this definition">¶</a></dt>
+<code class="descname">mean_std</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.mean_std" title="Permalink to this definition">¶</a></dt>
 <dd><p>H.mean_std() returns the mean and standard deviation of base parameters (order of base parameters:Shear,
 Stretch,Stagger,Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNA.plot">
-<tt class="descname">plot</tt><big>(</big><em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.plot" title="Permalink to this definition">¶</a></dt>
-<dd><p>Plot base parameter profiles  in a 1D graph
-(plotting of the mean and standard deviation parameter value for each individual base pair).</p>
+<code class="descname">plot</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.plot" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="docutils">
+<dt>Plot base parameter profiles  in a 1D graph</dt>
+<dd>(plotting of the mean and standard deviation parameter value for each individual base pair).</dd>
+</dl>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><em>Not available at this time</em></td>
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><em>Not available at this time</em></td>
 </tr>
 </tbody>
 </table>
@@ -299,14 +302,14 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNA.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNA.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNA.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Run X3DNA on the input file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNA.save">
-<tt class="descname">save</tt><big>(</big><em>filename='x3dna.pickle'</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.save" title="Permalink to this definition">¶</a></dt>
-<dd><p>Save <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.profiles" title="MDAnalysis.analysis.x3dna.X3DNA.profiles"><tt class="xref py py-attr docutils literal"><span class="pre">profiles</span></tt></a> as a Python pickle file <em>filename</em>.</p>
+<code class="descname">save</code><span class="sig-paren">(</span><em>filename='x3dna.pickle'</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.save" title="Permalink to this definition">¶</a></dt>
+<dd><p>Save <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.profiles" title="MDAnalysis.analysis.x3dna.X3DNA.profiles"><code class="xref py py-attr docutils literal"><span class="pre">profiles</span></code></a> as a Python pickle file <em>filename</em>.</p>
 <p>Load profiles dictionary with</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">cPickle</span>
 <span class="n">profiles</span> <span class="o">=</span> <span class="n">cPickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
@@ -316,14 +319,14 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNA.sorted_profiles_iter">
-<tt class="descname">sorted_profiles_iter</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.sorted_profiles_iter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sorted_profiles_iter</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.sorted_profiles_iter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return an iterator over profiles sorted by frame/order parameter <em>q</em>.</p>
-<p>The iterator produces tuples <tt class="docutils literal"><span class="pre">(q,</span> <span class="pre">profile)</span></tt>.</p>
+<p>The iterator produces tuples <code class="docutils literal"><span class="pre">(q,</span> <span class="pre">profile)</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNA.std">
-<tt class="descname">std</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.std" title="Permalink to this definition">¶</a></dt>
+<code class="descname">std</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNA.std" title="Permalink to this definition">¶</a></dt>
 <dd><p>H.std() returns the standard deviation of base parameters (order of base parameters:Shear,Stretch,Stagger,
 Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.</p>
 </dd></dl>
@@ -332,9 +335,9 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="class">
 <dt id="MDAnalysis.analysis.x3dna.X3DNAtraj">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.x3dna.</tt><tt class="descname">X3DNAtraj</tt><big>(</big><em>universe</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNAtraj"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.x3dna.</code><code class="descname">X3DNAtraj</code><span class="sig-paren">(</span><em>universe</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNAtraj"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj" title="Permalink to this definition">¶</a></dt>
 <dd><p>Analyze all frames in a trajectory.</p>
-<p>The <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA" title="MDAnalysis.analysis.x3dna.X3DNA"><tt class="xref py py-class docutils literal"><span class="pre">X3DNA</span></tt></a> class provides a direct interface to X3DNA. X3DNA itself
+<p>The <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA" title="MDAnalysis.analysis.x3dna.X3DNA"><code class="xref py py-class docutils literal"><span class="pre">X3DNA</span></code></a> class provides a direct interface to X3DNA. X3DNA itself
 has limited support for analysing trajectories but cannot deal with all the
 trajectory formats understood by MDAnalysis. This class can take any
 universe and feed it to X3DNA. By default it sequentially creates a PDB for
@@ -344,17 +347,17 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">The input trajectory as part of a
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>. trajectory is
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>. trajectory is
 converted to a sequence of PDB files and X3DNA is run on each
 individual file. (Use the <em>start</em>, <em>stop</em>, and <em>step</em> keywords
 to slice the trajectory.)</p>
 </dd>
 <dt><em>start</em>, <em>stop</em>, <em>step</em></dt>
 <dd><p class="first last">frame indices to slice the trajectory as
-<tt class="docutils literal"><span class="pre">universe.trajectory[start,</span> <span class="pre">stop,</span> <span class="pre">step]</span></tt></p>
+<code class="docutils literal"><span class="pre">universe.trajectory[start,</span> <span class="pre">stop,</span> <span class="pre">step]</span></code></p>
 </dd>
 <dt><em>x3dna_param</em></dt>
 <dd><p class="first last">indicates whether stacked bases or stacked base-pairs will be
@@ -362,7 +365,7 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 is True].</p>
 </dd>
 <dt><em>kwargs</em></dt>
-<dd><p class="first last">All other keywords are passed on to <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA" title="MDAnalysis.analysis.x3dna.X3DNA"><tt class="xref py py-class docutils literal"><span class="pre">X3DNA</span></tt></a> (see there for description).</p>
+<dd><p class="first last">All other keywords are passed on to <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA" title="MDAnalysis.analysis.x3dna.X3DNA"><code class="xref py py-class docutils literal"><span class="pre">X3DNA</span></code></a> (see there for description).</p>
 </dd>
 </dl>
 </td>
@@ -371,35 +374,37 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 </table>
 <dl class="attribute">
 <dt id="MDAnalysis.analysis.x3dna.X3DNAtraj.profiles">
-<tt class="descname">profiles</tt><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>After running <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.collect" title="MDAnalysis.analysis.x3dna.X3DNA.collect"><tt class="xref py py-meth docutils literal"><span class="pre">X3DNA.collect()</span></tt></a>, this dict contains all the
+<code class="descname">profiles</code><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.profiles" title="Permalink to this definition">¶</a></dt>
+<dd><p>After running <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNA.collect" title="MDAnalysis.analysis.x3dna.X3DNA.collect"><code class="xref py py-meth docutils literal"><span class="pre">X3DNA.collect()</span></code></a>, this dict contains all the
 X3DNA profiles, indexed by the frame number.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNAtraj.mean">
-<tt class="descname">mean</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.mean" title="Permalink to this definition">¶</a></dt>
+<code class="descname">mean</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.mean" title="Permalink to this definition">¶</a></dt>
 <dd><p>H.mean() returns the mean value for the base parameters (order of base parameters:Shear,Stretch,Stagger,
 Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNAtraj.mean_std">
-<tt class="descname">mean_std</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.mean_std" title="Permalink to this definition">¶</a></dt>
+<code class="descname">mean_std</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.mean_std" title="Permalink to this definition">¶</a></dt>
 <dd><p>H.mean_std() returns the mean and standard deviation of base parameters (order of base parameters:Shear,
 Stretch,Stagger,Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNAtraj.plot">
-<tt class="descname">plot</tt><big>(</big><em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.plot" title="Permalink to this definition">¶</a></dt>
-<dd><p>Plot base parameter profiles  in a 1D graph
-(plotting of the mean and standard deviation parameter value for each individual base pair).</p>
+<code class="descname">plot</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.plot" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="docutils">
+<dt>Plot base parameter profiles  in a 1D graph</dt>
+<dd>(plotting of the mean and standard deviation parameter value for each individual base pair).</dd>
+</dl>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><em>Not available at this time</em></td>
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><em>Not available at this time</em></td>
 </tr>
 </tbody>
 </table>
@@ -407,7 +412,7 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNAtraj.run">
-<tt class="descname">run</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNAtraj.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNAtraj.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.run" title="Permalink to this definition">¶</a></dt>
 <dd><p>Run X3DNA on the whole trajectory and collect profiles.</p>
 <p>Keyword arguments <em>start</em>, <em>stop</em>, and <em>step</em> can be used to only
 analyse part of the trajectory.</p>
@@ -415,14 +420,14 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNAtraj.run_x3dna">
-<tt class="descname">run_x3dna</tt><big>(</big><em>pdbfile</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNAtraj.run_x3dna"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.run_x3dna" title="Permalink to this definition">¶</a></dt>
+<code class="descname">run_x3dna</code><span class="sig-paren">(</span><em>pdbfile</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/x3dna.html#X3DNAtraj.run_x3dna"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.run_x3dna" title="Permalink to this definition">¶</a></dt>
 <dd><p>Run X3DNA on a single PDB file <em>pdbfile</em>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNAtraj.save">
-<tt class="descname">save</tt><big>(</big><em>filename='x3dna.pickle'</em><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.save" title="Permalink to this definition">¶</a></dt>
-<dd><p>Save <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.profiles" title="MDAnalysis.analysis.x3dna.X3DNAtraj.profiles"><tt class="xref py py-attr docutils literal"><span class="pre">profiles</span></tt></a> as a Python pickle file <em>filename</em>.</p>
+<code class="descname">save</code><span class="sig-paren">(</span><em>filename='x3dna.pickle'</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.save" title="Permalink to this definition">¶</a></dt>
+<dd><p>Save <a class="reference internal" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.profiles" title="MDAnalysis.analysis.x3dna.X3DNAtraj.profiles"><code class="xref py py-attr docutils literal"><span class="pre">profiles</span></code></a> as a Python pickle file <em>filename</em>.</p>
 <p>Load profiles dictionary with</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">cPickle</span>
 <span class="n">profiles</span> <span class="o">=</span> <span class="n">cPickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
@@ -432,14 +437,14 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNAtraj.sorted_profiles_iter">
-<tt class="descname">sorted_profiles_iter</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.sorted_profiles_iter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sorted_profiles_iter</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.sorted_profiles_iter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return an iterator over profiles sorted by frame/order parameter <em>q</em>.</p>
-<p>The iterator produces tuples <tt class="docutils literal"><span class="pre">(q,</span> <span class="pre">profile)</span></tt>.</p>
+<p>The iterator produces tuples <code class="docutils literal"><span class="pre">(q,</span> <span class="pre">profile)</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.analysis.x3dna.X3DNAtraj.std">
-<tt class="descname">std</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.std" title="Permalink to this definition">¶</a></dt>
+<code class="descname">std</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.analysis.x3dna.X3DNAtraj.std" title="Permalink to this definition">¶</a></dt>
 <dd><p>H.std() returns the standard deviation of base parameters (order of base parameters:Shear,Stretch,Stagger,
 Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.</p>
 </dd></dl>
@@ -451,11 +456,12 @@ <h2>3.4.2.2. Analysis<a class="headerlink" href="#analysis" title="Permalink to
 <h2>3.4.2.3. Utilities<a class="headerlink" href="#utilities" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.analysis.x3dna.ApplicationError">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.analysis.x3dna.</tt><tt class="descname">ApplicationError</tt><a class="headerlink" href="#MDAnalysis.analysis.x3dna.ApplicationError" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.analysis.x3dna.</code><code class="descname">ApplicationError</code><a class="reference internal" href="../../_modules/MDAnalysis/exceptions.html#ApplicationError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.analysis.x3dna.ApplicationError" title="Permalink to this definition">¶</a></dt>
 <dd><p>Raised when an external application failed.</p>
 <p>The error code is specific for the application.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 </div>
@@ -467,7 +473,7 @@ <h2>3.4.2.3. Utilities<a class="headerlink" href="#utilities" title="Permalink t
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -482,11 +488,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="nuclinfo.html" title="3.4.1. Nucleic acid analysis — MDAnalysis.analysis.nuclinfo"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../analysis_modules.html" >3. Analysis modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -496,7 +502,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis_modules.html b/package/doc/html/documentation_pages/analysis_modules.html
index 7f20c39a1b7..1bb366aaf3f 100644
--- a/package/doc/html/documentation_pages/analysis_modules.html
+++ b/package/doc/html/documentation_pages/analysis_modules.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3. Analysis modules &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>3. Analysis modules &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="3.1.1. Coordinate fitting and alignment — MDAnalysis.analysis.align" href="analysis/align.html" />
     <link rel="prev" title="2. Selection Commands" href="selections.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -50,10 +48,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="selections.html" title="2. Selection Commands"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../index.html">
               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -61,24 +59,12 @@ <h3>Navigation</h3>
   <h3><a href="../index.html">Table Of Contents</a></h3>
   <ul>
 <li><a class="reference internal" href="#">3. Analysis modules</a><ul>
-<li><a class="reference internal" href="#distances-and-contacts">3.1. Distances and contacts</a><ul>
-</ul>
-</li>
-<li><a class="reference internal" href="#hydrogen-bonding">3.2. Hydrogen bonding</a><ul>
-</ul>
-</li>
-<li><a class="reference internal" href="#membranes-and-membrane-proteins">3.3. Membranes and membrane proteins</a><ul>
-</ul>
-</li>
-<li><a class="reference internal" href="#nucleic-acids">3.4. Nucleic acids</a><ul>
-</ul>
-</li>
-<li><a class="reference internal" href="#structure">3.5. Structure</a><ul>
-</ul>
-</li>
-<li><a class="reference internal" href="#volumetric-analysis">3.6. Volumetric analysis</a><ul>
-</ul>
-</li>
+<li><a class="reference internal" href="#distances-and-contacts">3.1. Distances and contacts</a></li>
+<li><a class="reference internal" href="#hydrogen-bonding">3.2. Hydrogen bonding</a></li>
+<li><a class="reference internal" href="#membranes-and-membrane-proteins">3.3. Membranes and membrane proteins</a></li>
+<li><a class="reference internal" href="#nucleic-acids">3.4. Nucleic acids</a></li>
+<li><a class="reference internal" href="#structure">3.5. Structure</a></li>
+<li><a class="reference internal" href="#volumetric-analysis">3.6. Volumetric analysis</a></li>
 </ul>
 </li>
 </ul>
@@ -88,13 +74,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">2. Selection Commands</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="analysis/align.html"
-                        title="next chapter">3.1.1. Coordinate fitting and alignment &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.align</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/analysis_modules.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">3.1.1. Coordinate fitting and alignment &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.align</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/analysis_modules.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -113,11 +101,11 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="analysis-modules">
 <h1>3. Analysis modules<a class="headerlink" href="#analysis-modules" title="Permalink to this headline">¶</a></h1>
-<p>The <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis</span></tt> module contains code to carry out
+<p>The <code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis</span></code> module contains code to carry out
 specific analysis functionality. It is based on the core functionality
 (i.e. trajectory I/O, selections etc). The analysis modules can be
 used as examples for how to use MDAnalysis but also as working code
@@ -126,27 +114,27 @@ <h1>3. Analysis modules<a class="headerlink" href="#analysis-modules" title="Per
 <p>Please see the individual module documentation for additional
 references and citation information.</p>
 <p>These modules are not imported by default; in order to use them one
-has to import them from <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis</span></tt>, for instance</p>
+has to import them from <code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis</span></code>, for instance</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">MDAnalysis.analysis.align</span>
 </pre></div>
 </div>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">Some of the modules require additional Python packages such as
-<tt class="xref py py-mod docutils literal"><span class="pre">scipy</span></tt> from the <a class="reference external" href="http://www.scipy.org/">SciPy</a> package or <tt class="xref py py-mod docutils literal"><span class="pre">networkx</span></tt> from
+<code class="xref py py-mod docutils literal"><span class="pre">scipy</span></code> from the <a class="reference external" href="http://www.scipy.org/">SciPy</a> package or <code class="xref py py-mod docutils literal"><span class="pre">networkx</span></code> from
 <a class="reference external" href="http://networkx.lanl.gov/">NetworkX</a>. These package are <em>not automatically installed</em> (although
-one can add the <tt class="docutils literal"><span class="pre">[analysis]</span></tt> requirement to the
+one can add the <code class="docutils literal"><span class="pre">[analysis]</span></code> requirement to the
 <strong class="program">easy_install</strong> command line to force their installation.</p>
 </div>
 <div class="section" id="distances-and-contacts">
 <h2>3.1. Distances and contacts<a class="headerlink" href="#distances-and-contacts" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="analysis/align.html">3.1.1. Coordinate fitting and alignment &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.align</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="analysis/contacts.html">3.1.2. Native contacts analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="analysis/distances.html">3.1.3. Distance analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.distances</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="analysis/rms.html">3.1.4. Calculating root mean square quantities &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="analysis/psa.html">3.1.5. Calculating path similarity &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.psa</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/align.html">3.1.1. Coordinate fitting and alignment &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.align</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/contacts.html">3.1.2. Native contacts analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/distances.html">3.1.3. Distance analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.distances</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/rms.html">3.1.4. Calculating root mean square quantities &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/psa.html">3.1.5. Calculating path similarity &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.psa</span></code></a></li>
 </ul>
 </div>
 </div>
@@ -154,8 +142,8 @@ <h2>3.1. Distances and contacts<a class="headerlink" href="#distances-and-contac
 <h2>3.2. Hydrogen bonding<a class="headerlink" href="#hydrogen-bonding" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="analysis/hbond_analysis.html">3.2.1. Hydrogen Bond analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_analysis</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="analysis/hbond_autocorrel.html">3.2.2. Hydrogen bond autocorrelation &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_autocorrel</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/hbond_analysis.html">3.2.1. Hydrogen Bond analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_analysis</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/hbond_autocorrel.html">3.2.2. Hydrogen bond autocorrelation &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds.hbond_autocorrel</span></code></a></li>
 </ul>
 </div>
 </div>
@@ -163,8 +151,8 @@ <h2>3.2. Hydrogen bonding<a class="headerlink" href="#hydrogen-bonding" title="P
 <h2>3.3. Membranes and membrane proteins<a class="headerlink" href="#membranes-and-membrane-proteins" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="analysis/hole.html">3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.hole</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="analysis/leaflet.html">3.3.2. Leaflet identification &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.leaflet</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/hole.html">3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.hole</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/leaflet.html">3.3.2. Leaflet identification &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.leaflet</span></code></a></li>
 </ul>
 </div>
 </div>
@@ -172,8 +160,8 @@ <h2>3.3. Membranes and membrane proteins<a class="headerlink" href="#membranes-a
 <h2>3.4. Nucleic acids<a class="headerlink" href="#nucleic-acids" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="analysis/nuclinfo.html">3.4.1. Nucleic acid analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.nuclinfo</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="analysis/x3dna.html">3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.x3dna</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/nuclinfo.html">3.4.1. Nucleic acid analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.nuclinfo</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/x3dna.html">3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.x3dna</span></code></a></li>
 </ul>
 </div>
 </div>
@@ -181,7 +169,7 @@ <h2>3.4. Nucleic acids<a class="headerlink" href="#nucleic-acids" title="Permali
 <h2>3.5. Structure<a class="headerlink" href="#structure" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="analysis/gnm.html">3.5.1. Elastic network analysis of MD trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.gnm</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/gnm.html">3.5.1. Elastic network analysis of MD trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.gnm</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="analysis/helanal.html">3.5.2. HELANAL &#8212; analysis of protein helices</a></li>
 </ul>
 </div>
@@ -190,8 +178,8 @@ <h2>3.5. Structure<a class="headerlink" href="#structure" title="Permalink to th
 <h2>3.6. Volumetric analysis<a class="headerlink" href="#volumetric-analysis" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="analysis/density.html">3.6.1. Generating densities from trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.density</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="analysis/waterdynamics.html">3.6.2. Water dynamics analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/density.html">3.6.1. Generating densities from trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.density</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis/waterdynamics.html">3.6.2. Water dynamics analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></code></a></li>
 </ul>
 </div>
 </div>
@@ -203,7 +191,7 @@ <h2>3.6. Volumetric analysis<a class="headerlink" href="#volumetric-analysis" ti
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -218,10 +206,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="selections.html" title="2. Selection Commands"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -231,7 +219,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/CRD.html b/package/doc/html/documentation_pages/coordinates/CRD.html
index 38b1355df73..cea693066a0 100644
--- a/package/doc/html/documentation_pages/coordinates/CRD.html
+++ b/package/doc/html/documentation_pages/coordinates/CRD.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.2. CRD structure files in MDAnalysis — MDAnalysis.coordinates.CRD &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.2. CRD structure files in MDAnalysis — MDAnalysis.coordinates.CRD &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.3. DCD trajectory I/O — MDAnalysis.coordinates.DCD" href="DCD.html" />
     <link rel="prev" title="5.1. Trajectory Readers and Writers — MDAnalysis.coordinates" href="init.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="init.html" title="5.1. Trajectory Readers and Writers — MDAnalysis.coordinates"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="init.html"
-                        title="previous chapter">5.1. Trajectory Readers and Writers  &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates</span></tt></a></p>
+                        title="previous chapter">5.1. Trajectory Readers and Writers  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="DCD.html"
-                        title="next chapter">5.3. DCD trajectory I/O  &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/CRD.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.3. DCD trajectory I/O  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/CRD.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,35 +90,36 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.CRD"></span><div class="section" id="crd-structure-files-in-mdanalysis-mdanalysis-coordinates-crd">
-<h1>5.2. CRD structure files in MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.CRD" title="MDAnalysis.coordinates.CRD"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.CRD</span></tt></a><a class="headerlink" href="#crd-structure-files-in-mdanalysis-mdanalysis-coordinates-crd" title="Permalink to this headline">¶</a></h1>
+<h1>5.2. CRD structure files in MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.CRD" title="MDAnalysis.coordinates.CRD"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.CRD</span></code></a><a class="headerlink" href="#crd-structure-files-in-mdanalysis-mdanalysis-coordinates-crd" title="Permalink to this headline">¶</a></h1>
 <p>Read and write coordinates in CHARMM CARD coordinate format (suffix
 &#8220;crd&#8221;). The CHARMM &#8220;extended format&#8221; is handled automatically.</p>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.CRD.CRDReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.CRD.</tt><tt class="descname">CRDReader</tt><big>(</big><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/CRD.html#CRDReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.CRD.CRDReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.CRD.</code><code class="descname">CRDReader</code><span class="sig-paren">(</span><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/CRD.html#CRDReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.CRD.CRDReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>CRD reader that implements the standard and extended CRD coordinate formats</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now returns a ValueError instead of FormatError
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now returns a ValueError instead of FormatError
 Frames now 0-based instead of 1-based</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.CRD.CRDReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/CRD.html#CRDReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.CRD.CRDReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/CRD.html#CRDReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.CRD.CRDReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a CRDWriter for <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output CRD file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.CRD.CRDWriter" title="MDAnalysis.coordinates.CRD.CRDWriter"><tt class="xref py py-class docutils literal"><span class="pre">CRDWriter</span></tt></a></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.CRD.CRDWriter" title="MDAnalysis.coordinates.CRD.CRDWriter"><code class="xref py py-class docutils literal"><span class="pre">CRDWriter</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -129,15 +130,16 @@ <h1>5.2. CRD structure files in MDAnalysis &#8212; <a class="reference internal"
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.CRD.CRDWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.CRD.</tt><tt class="descname">CRDWriter</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/CRD.html#CRDWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.CRD.CRDWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.CRD.</code><code class="descname">CRDWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/CRD.html#CRDWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.CRD.CRDWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>CRD writer that implements the CHARMM CRD coordinate format.</p>
 <p>It automatically writes the CHARMM EXT extended format if there
 are more than 99,999 atoms.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.CRD.CRDWriter.write">
-<tt class="descname">write</tt><big>(</big><em>selection</em>, <em>frame=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/CRD.html#CRDWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.CRD.CRDWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>selection</em>, <em>frame=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/CRD.html#CRDWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.CRD.CRDWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write selection at current trajectory frame to file.</p>
 <p>write(selection,frame=FRAME)</p>
 <p>selection         MDAnalysis AtomGroup
@@ -154,7 +156,7 @@ <h1>5.2. CRD structure files in MDAnalysis &#8212; <a class="reference internal"
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -169,11 +171,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="init.html" title="5.1. Trajectory Readers and Writers — MDAnalysis.coordinates"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -183,7 +185,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/DCD.html b/package/doc/html/documentation_pages/coordinates/DCD.html
index 4e1a5c61e4a..a077a0bf887 100644
--- a/package/doc/html/documentation_pages/coordinates/DCD.html
+++ b/package/doc/html/documentation_pages/coordinates/DCD.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.3. DCD trajectory I/O — MDAnalysis.coordinates.DCD &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.3. DCD trajectory I/O — MDAnalysis.coordinates.DCD &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly" href="DLPoly.html" />
     <link rel="prev" title="5.2. CRD structure files in MDAnalysis — MDAnalysis.coordinates.CRD" href="CRD.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="CRD.html" title="5.2. CRD structure files in MDAnalysis — MDAnalysis.coordinates.CRD"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.3. DCD trajectory I/O  &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.3. DCD trajectory I/O  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></code></a><ul>
 <li><a class="reference internal" href="#classes">5.3.1. Classes</a></li>
 </ul>
 </li>
@@ -70,16 +68,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="CRD.html"
-                        title="previous chapter">5.2. CRD structure files in MDAnalysis &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.CRD</span></tt></a></p>
+                        title="previous chapter">5.2. CRD structure files in MDAnalysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.CRD</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="DLPoly.html"
-                        title="next chapter">5.4. DL_Poly format reader <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.DLPoly</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/DCD.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.4. DL_Poly format reader <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.DLPoly</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/DCD.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,18 +98,18 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.DCD"></span><div class="section" id="dcd-trajectory-i-o-mdanalysis-coordinates-dcd">
-<h1>5.3. DCD trajectory I/O  &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.DCD" title="MDAnalysis.coordinates.DCD"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></tt></a><a class="headerlink" href="#dcd-trajectory-i-o-mdanalysis-coordinates-dcd" title="Permalink to this headline">¶</a></h1>
+<h1>5.3. DCD trajectory I/O  &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.DCD" title="MDAnalysis.coordinates.DCD"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></code></a><a class="headerlink" href="#dcd-trajectory-i-o-mdanalysis-coordinates-dcd" title="Permalink to this headline">¶</a></h1>
 <p>Classes to read and write DCD binary trajectories, the format used by
 CHARMM, NAMD, and also LAMMPS. Trajectories can be read regardless of
 system-endianness as this is auto-detected.</p>
 <p>Generally, DCD trajectories produced by any code can be read (with the
-<a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDReader" title="MDAnalysis.coordinates.DCD.DCDReader"><tt class="xref py py-class docutils literal"><span class="pre">DCDReader</span></tt></a>) although there can be issues with the unitcell
+<a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDReader" title="MDAnalysis.coordinates.DCD.DCDReader"><code class="xref py py-class docutils literal"><span class="pre">DCDReader</span></code></a>) although there can be issues with the unitcell
 (simulation box) representation (see
-<a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="MDAnalysis.coordinates.DCD.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></tt></a>). DCDs can also be written but the
-<a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDWriter" title="MDAnalysis.coordinates.DCD.DCDWriter"><tt class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></tt></a> follows recent NAMD/VMD convention for the unitcell
+<a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="MDAnalysis.coordinates.DCD.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></code></a>). DCDs can also be written but the
+<a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDWriter" title="MDAnalysis.coordinates.DCD.DCDWriter"><code class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></code></a> follows recent NAMD/VMD convention for the unitcell
 but still writes AKMA time. Reading and writing these trajectories
 within MDAnalysis will work seamlessly but if you process those
 trajectories with other tools you might need to watch out that time
@@ -120,16 +120,16 @@ <h1>5.3. DCD trajectory I/O  &#8212; <a class="reference internal" href="#module
 CHARMM use it differently. Currently, MDAnalysis tries to guess the
 correct <strong>format for the unitcell representation</strong> but it can be
 wrong. <strong>Check the unitcell dimensions</strong>, especially for triclinic
-unitcells (see <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/187">Issue 187</a> and <a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="MDAnalysis.coordinates.DCD.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></tt></a>). A
+unitcells (see <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/187">Issue 187</a> and <a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="MDAnalysis.coordinates.DCD.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></code></a>). A
 second potential issue are the units of time which are AKMA for the
-<a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDReader" title="MDAnalysis.coordinates.DCD.DCDReader"><tt class="xref py py-class docutils literal"><span class="pre">DCDReader</span></tt></a> (following CHARMM) but ps for NAMD. As a
+<a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDReader" title="MDAnalysis.coordinates.DCD.DCDReader"><code class="xref py py-class docutils literal"><span class="pre">DCDReader</span></code></a> (following CHARMM) but ps for NAMD. As a
 workaround one can employ the configurable
-<a class="reference internal" href="LAMMPS.html#MDAnalysis.coordinates.LAMMPS.DCDReader" title="MDAnalysis.coordinates.LAMMPS.DCDReader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS.DCDReader</span></tt></a> for NAMD
+<a class="reference internal" href="LAMMPS.html#MDAnalysis.coordinates.LAMMPS.DCDReader" title="MDAnalysis.coordinates.LAMMPS.DCDReader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS.DCDReader</span></code></a> for NAMD
 trajectories.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last">The <a class="reference internal" href="LAMMPS.html#module-MDAnalysis.coordinates.LAMMPS" title="MDAnalysis.coordinates.LAMMPS"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></tt></a> module provides
+<p class="last">The <a class="reference internal" href="LAMMPS.html#module-MDAnalysis.coordinates.LAMMPS" title="MDAnalysis.coordinates.LAMMPS"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></code></a> module provides
 a more flexible DCD reader/writer.</p>
 </div>
 <p>The classes in this module are the reference implementations for the
@@ -138,31 +138,31 @@ <h1>5.3. DCD trajectory I/O  &#8212; <a class="reference internal" href="#module
 <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.DCD.Timestep">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.DCD.</tt><tt class="descname">Timestep</tt><big>(</big><em>n_atoms</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.DCD.</code><code class="descname">Timestep</code><span class="sig-paren">(</span><em>n_atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a Timestep, representing a frame of a trajectory</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">The total number of atoms this Timestep describes</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>positions</em></dt>
-<dd><p class="first last">Whether this Timestep has position information [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has position information [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 <dt><em>velocities</em></dt>
-<dd><p class="first last">Whether this Timestep has velocity information [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has velocity information [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>forces</em></dt>
-<dd><p class="first last">Whether this Timestep has force information [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has force information [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>dt</em></dt>
-<dd><p class="first last">The time difference between frames (ps).  If <a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.time" title="MDAnalysis.coordinates.DCD.Timestep.time"><tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt></a>
+<dd><p class="first last">The time difference between frames (ps).  If <a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.time" title="MDAnalysis.coordinates.DCD.Timestep.time"><code class="xref py py-attr docutils literal"><span class="pre">time</span></code></a>
 is set, then <cite>dt</cite> will be ignored.</p>
 </dd>
 <dt><em>time_offset</em></dt>
@@ -173,27 +173,28 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Added keywords for positions, velocities and forces
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Added keywords for positions, velocities and forces
 Can add and remove position/velocity/force information by using
 the has_* attribute</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.copy">
-<tt class="descname">copy</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.copy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep" title="MDAnalysis.coordinates.DCD.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>.</p>
+<code class="descname">copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep" title="MDAnalysis.coordinates.DCD.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.copy_slice">
-<tt class="descname">copy_slice</tt><big>(</big><em>sel</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
+<code class="descname">copy_slice</code><span class="sig-paren">(</span><em>sel</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy_slice"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
 <dd><p>Make a new Timestep containing a subset of the original Timestep.</p>
-<p><tt class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></tt>
-<tt class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></tt></p>
+<p><code class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></code>
+<code class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></code></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A Timestep object of the same type containing all header
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A Timestep object of the same type containing all header
 information and all atom information relevant to the selection.</td>
 </tr>
 </tbody>
@@ -203,26 +204,28 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 <p class="last">The selection must be a 0 based slice or array of the atom indices
 in this Timestep</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
 copy official attributes of the Timestep.</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.dimensions">
-<tt class="descname">dimensions</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#Timestep.dimensions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>unitcell dimensions (<em>A</em>, <em>B</em>, <em>C</em>, <em>alpha</em>, <em>beta</em>, <em>gamma</em>)</p>
 <p>lengths <em>A</em>, <em>B</em>, <em>C</em> are in the MDAnalysis length unit (Å), and
 angles are in degrees.</p>
-<p><a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="MDAnalysis.coordinates.DCD.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">dimensions</span></tt></a> is read-only because it transforms the actual format
+<p><a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="MDAnalysis.coordinates.DCD.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">dimensions</span></code></a> is read-only because it transforms the actual format
 of the unitcell (which differs between different trajectory formats) to
 the representation described here, which is used everywhere in
 MDAnalysis.</p>
 <p>The ordering of the angles in the unitcell is the same as in recent
 versions of VMD&#8217;s <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/dcdplugin_8c-source.html#l00947">DCDplugin</a> (2013), namely the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html">X-PLOR DCD format</a>:
-The original unitcell is read as <tt class="docutils literal"><span class="pre">[A,</span> <span class="pre">gamma,</span> <span class="pre">B,</span> <span class="pre">beta,</span> <span class="pre">alpha,</span> <span class="pre">C]</span></tt> from
+The original unitcell is read as <code class="docutils literal"><span class="pre">[A,</span> <span class="pre">gamma,</span> <span class="pre">B,</span> <span class="pre">beta,</span> <span class="pre">alpha,</span> <span class="pre">C]</span></code> from
 the DCD file (actually, the direction cosines are stored instead of the
 angles but the underlying C code already does this conversion); if any
 of these values are &lt; 0 or if any of the angles are &gt; 180 degrees then
@@ -237,28 +240,30 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 and tries to guess the new CHARMM one. Old CHARMM trajectories might
 give wrong unitcell values. For more details see <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/187">Issue 187</a>.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Unitcell is now interpreted in the newer NAMD DCD format as <tt class="docutils literal"><span class="pre">[A,</span>
-<span class="pre">gamma,</span> <span class="pre">B,</span> <span class="pre">beta,</span> <span class="pre">alpha,</span> <span class="pre">C]</span></tt> instead of the old MDAnalysis/CHARMM
-ordering <tt class="docutils literal"><span class="pre">[A,</span> <span class="pre">alpha,</span> <span class="pre">B,</span> <span class="pre">beta,</span> <span class="pre">gamma,</span> <span class="pre">C]</span></tt>. We attempt to detect the
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Unitcell is now interpreted in the newer NAMD DCD format as <code class="docutils literal"><span class="pre">[A,</span>
+<span class="pre">gamma,</span> <span class="pre">B,</span> <span class="pre">beta,</span> <span class="pre">alpha,</span> <span class="pre">C]</span></code> instead of the old MDAnalysis/CHARMM
+ordering <code class="docutils literal"><span class="pre">[A,</span> <span class="pre">alpha,</span> <span class="pre">B,</span> <span class="pre">beta,</span> <span class="pre">gamma,</span> <span class="pre">C]</span></code>. We attempt to detect the
 new CHARMM DCD unitcell format (see <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/187">Issue 187</a> for a discussion).</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.dt" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dt</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.dt" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time difference in ps between timesteps</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">This defaults to 1.0 ps in the absence of time data</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.forces">
-<tt class="descname">forces</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.forces" title="Permalink to this definition">¶</a></dt>
+<code class="descname">forces</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.forces" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the forces of all atoms in this Timestep</p>
 <p>Setting this attribute will add forces to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -266,12 +271,12 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of force data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of force data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.NoDataError</span></tt></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.NoDataError</span></code></dt>
 <dd><p class="first last">When the Timestep does not contain force information</p>
 </dd>
 </dl>
@@ -279,67 +284,74 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
-<dl class="classmethod">
+<dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.from_coordinates">
-<em class="property">classmethod </em><tt class="descname">from_coordinates</tt><big>(</big><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
+<code class="descname">from_coordinates</code><span class="sig-paren">(</span><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_coordinates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create an instance of this Timestep, from coordinate data</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
-<dl class="classmethod">
+<dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.from_timestep">
-<em class="property">classmethod </em><tt class="descname">from_timestep</tt><big>(</big><em>other</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">from_timestep</code><span class="sig-paren">(</span><em>other</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a copy of another Timestep, in the format of this Timestep</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.has_forces">
-<tt class="descname">has_forces</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.has_forces" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_forces</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.has_forces" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has force data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.has_positions">
-<tt class="descname">has_positions</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.has_positions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_positions</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.has_positions" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has position data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.has_velocities">
-<tt class="descname">has_velocities</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.has_velocities" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_velocities</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.has_velocities" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has velocity data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.n_atoms">
-<tt class="descname">n_atoms</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>A read only view of the number of atoms this Timestep has</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.positions">
-<tt class="descname">positions</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.positions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">positions</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.positions" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the positions of all atoms in this Timestep</p>
 <p>Setting this attribute will add positions to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -347,12 +359,12 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of position data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of position data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></tt></a></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></code></a></dt>
 <dd><p class="first last">If the Timestep has no position data</p>
 </dd>
 </dl>
@@ -360,13 +372,14 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now can raise NoDataError when no position data present</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now can raise NoDataError when no position data present</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time in ps of this timestep</p>
 <p>This is calculated as:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">time</span>
@@ -376,19 +389,20 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span> <span class="o">*</span> <span class="n">ts</span><span class="o">.</span><span class="n">dt</span>
 </pre></div>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.triclinic_dimensions">
-<tt class="descname">triclinic_dimensions</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">triclinic_dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>The unitcell dimensions represented as triclinic vectors</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
 </tr>
 </tbody>
 </table>
@@ -408,17 +422,18 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 <span class="go">        72.45159912,  71.56504822], dtype=float32)</span>
 </pre></div>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.velocities">
-<tt class="descname">velocities</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.velocities" title="Permalink to this definition">¶</a></dt>
+<code class="descname">velocities</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.velocities" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the velocities of all atoms in this Timestep</p>
 <p>Setting this attribute will add velocities to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -426,12 +441,12 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of velocity data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of velocity data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></tt></a></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></code></a></dt>
 <dd><p class="first last">When the Timestep does not contain velocity information</p>
 </dd>
 </dl>
@@ -439,13 +454,14 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.Timestep.volume">
-<tt class="descname">volume</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.volume" title="Permalink to this definition">¶</a></dt>
+<code class="descname">volume</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.Timestep.volume" title="Permalink to this definition">¶</a></dt>
 <dd><p>volume of the unitcell</p>
 </dd></dl>
 
@@ -453,40 +469,40 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.DCD.</tt><tt class="descname">DCDReader</tt><big>(</big><em>dcdfilename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.DCD.</code><code class="descname">DCDReader</code><span class="sig-paren">(</span><em>dcdfilename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reads from a DCD file</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Data :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Data:</th><td class="field-body"><dl class="first docutils">
 <dt>ts</dt>
-<dd><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep" title="MDAnalysis.coordinates.DCD.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> object containing coordinates of current frame</p>
+<dd><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep" title="MDAnalysis.coordinates.DCD.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> object containing coordinates of current frame</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Methods :</th><td class="field-body"><dl class="first last docutils">
-<dt><tt class="docutils literal"><span class="pre">dcd</span> <span class="pre">=</span> <span class="pre">DCD(dcdfilename)</span></tt></dt>
+<tr class="field-even field"><th class="field-name">Methods:</th><td class="field-body"><dl class="first last docutils">
+<dt><code class="docutils literal"><span class="pre">dcd</span> <span class="pre">=</span> <span class="pre">DCD(dcdfilename)</span></code></dt>
 <dd><p class="first last">open dcd file and read header</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">len(dcd)</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">len(dcd)</span></code></dt>
 <dd><p class="first last">return number of frames in dcd</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">dcd:</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">dcd:</span></code></dt>
 <dd><p class="first last">iterate through trajectory</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">dcd[start:stop:skip]:</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">dcd[start:stop:skip]:</span></code></dt>
 <dd><p class="first last">iterate through a trajectory</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">dcd[i]</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">dcd[i]</span></code></dt>
 <dd><p class="first last">random access into the trajectory (i corresponds to frame number)</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">data</span> <span class="pre">=</span> <span class="pre">dcd.timeseries(...)</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">data</span> <span class="pre">=</span> <span class="pre">dcd.timeseries(...)</span></code></dt>
 <dd><p class="first last">retrieve a subset of coordinate information for a group of atoms</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">data</span> <span class="pre">=</span> <span class="pre">dcd.correl(...)</span></tt></dt>
-<dd><p class="first last">populate a <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.Timeseries.Collection</span></tt> object with computed timeseries</p>
+<dt><code class="docutils literal"><span class="pre">data</span> <span class="pre">=</span> <span class="pre">dcd.correl(...)</span></code></dt>
+<dd><p class="first last">populate a <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.Timeseries.Collection</span></code> object with computed timeseries</p>
 </dd>
 </dl>
 </td>
@@ -500,47 +516,49 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 guess the correct format for the unitcell representation but it
 can be wrong. <strong>Check the unitcell dimensions</strong>, especially for
 triclinic unitcells (see <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/187">Issue 187</a> and
-<a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="MDAnalysis.coordinates.DCD.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></tt></a>). A second potential issue are the
+<a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="MDAnalysis.coordinates.DCD.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></code></a>). A second potential issue are the
 units of time (TODO).</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>The underlying DCD reader (written in C and derived from the
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>The underlying DCD reader (written in C and derived from the
 catdcd/molfile plugin code of VMD) is now reading the unitcell in
-NAMD ordering: <tt class="docutils literal"><span class="pre">[A,</span> <span class="pre">B,</span> <span class="pre">C,</span> <span class="pre">sin(gamma),</span> <span class="pre">sin(beta),</span>
-<span class="pre">sin(alpha)]</span></tt>. See <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/187">Issue 187</a> for further details.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based
+NAMD ordering: <code class="docutils literal"><span class="pre">[A,</span> <span class="pre">B,</span> <span class="pre">C,</span> <span class="pre">sin(gamma),</span> <span class="pre">sin(beta),</span>
+<span class="pre">sin(alpha)]</span></code>. See <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/187">Issue 187</a> for further details.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based
 Native frame number read into ts._frame
 Removed skip keyword and functionality</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.OtherWriter">
-<tt class="descname">OtherWriter</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">OtherWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a writer appropriate for <em>filename</em>.</p>
 <p>Sets the default keywords <em>start</em>, <em>step</em> and <em>dt</em> (if
-available). <em>n_atoms</em> is always set from <tt class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></tt>.</p>
-<div class="admonition-see-also admonition seealso">
+available). <em>n_atoms</em> is always set from <code class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></code>.</p>
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></tt> and <tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></tt></p>
+<p class="last"><code class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></code> and <code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a DCDWriter for <em>filename</em> with the same parameters as this DCD.</p>
 <p>All values can be changed through keyword arguments.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output DCD trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">number of atoms</p>
 </dd>
@@ -555,8 +573,8 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </dd>
 <dt><em>dt</em></dt>
 <dd><p class="first last"><strong>Override</strong> <em>step</em> and <em>delta</em> so that the DCD records that <em>dt</em> ps
-lie between two frames. (It sets <em>step</em> = 1 and <em>delta</em> = <tt class="docutils literal"><span class="pre">AKMA(dt)</span></tt>.)
-The default is <tt class="docutils literal"><span class="pre">None</span></tt>, in which case <em>step</em> and <em>delta</em> are used.</p>
+lie between two frames. (It sets <em>step</em> = 1 and <em>delta</em> = <code class="docutils literal"><span class="pre">AKMA(dt)</span></code>.)
+The default is <code class="docutils literal"><span class="pre">None</span></code>, in which case <em>step</em> and <em>delta</em> are used.</p>
 </dd>
 <dt><em>remarks</em></dt>
 <dd><p class="first last">string that is stored in the DCD header [XXX &#8211; max length?]</p>
@@ -564,7 +582,7 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDWriter" title="MDAnalysis.coordinates.DCD.DCDWriter"><tt class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></tt></a></p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDWriter" title="MDAnalysis.coordinates.DCD.DCDWriter"><code class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -575,113 +593,121 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 according to the CHARMM format. The time between two frames would be
 <em>delta</em> * <em>step</em> !</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDWriter" title="MDAnalysis.coordinates.DCD.DCDWriter"><tt class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></tt></a> has detailed argument description</p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDWriter" title="MDAnalysis.coordinates.DCD.DCDWriter"><code class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></code></a> has detailed argument description</p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.correl">
-<tt class="descname">correl</tt><big>(</big><em>timeseries</em>, <em>start=0</em>, <em>stop=-1</em>, <em>skip=1</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDReader.correl"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.correl" title="Permalink to this definition">¶</a></dt>
+<code class="descname">correl</code><span class="sig-paren">(</span><em>timeseries</em>, <em>start=0</em>, <em>stop=-1</em>, <em>skip=1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDReader.correl"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.correl" title="Permalink to this definition">¶</a></dt>
 <dd><p>Populate a TimeseriesCollection object with timeseries computed from the trajectory</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>timeseries</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/Timeseries.html#MDAnalysis.core.Timeseries.TimeseriesCollection" title="MDAnalysis.core.Timeseries.TimeseriesCollection"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.Timeseries.TimeseriesCollection</span></tt></a></p>
+<dd><p class="first last"><a class="reference internal" href="../core/Timeseries.html#MDAnalysis.core.Timeseries.TimeseriesCollection" title="MDAnalysis.core.Timeseries.TimeseriesCollection"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.Timeseries.TimeseriesCollection</span></code></a></p>
 </dd>
 <dt><em>start, stop, skip</em></dt>
 <dd><p class="first last">subset of trajectory to use, with start and stop being inclusive</p>
@@ -695,42 +721,42 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.frame">
-<tt class="descname">frame</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.frame" title="Permalink to this definition">¶</a></dt>
+<code class="descname">frame</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.frame" title="Permalink to this definition">¶</a></dt>
 <dd><p>Frame number of the current time step.</p>
-<p>This is a simple short cut to <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt>.</p>
+<p>This is a simple short cut to <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.next">
-<tt class="descname">next</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.next" title="Permalink to this definition">¶</a></dt>
+<code class="descname">next</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.next" title="Permalink to this definition">¶</a></dt>
 <dd><p>Forward one step to next frame.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.rewind">
-<tt class="descname">rewind</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.rewind" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rewind</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.rewind" title="Permalink to this definition">¶</a></dt>
 <dd><p>Position at beginning of trajectory</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>Time of the current frame in MDAnalysis time units (typically ps).</p>
 <p>This is either read straight from the Timestep, or calculated as
-time = <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt> * <a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dt" title="MDAnalysis.coordinates.DCD.Timestep.dt"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></tt></a></p>
+time = <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code> * <a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dt" title="MDAnalysis.coordinates.DCD.Timestep.dt"><code class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></code></a></p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.timeseries">
-<tt class="descname">timeseries</tt><big>(</big><em>asel</em>, <em>start=0</em>, <em>stop=-1</em>, <em>skip=1</em>, <em>format=u'afc'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDReader.timeseries"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.timeseries" title="Permalink to this definition">¶</a></dt>
+<code class="descname">timeseries</code><span class="sig-paren">(</span><em>asel</em>, <em>start=0</em>, <em>stop=-1</em>, <em>skip=1</em>, <em>format=u'afc'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDReader.timeseries"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.timeseries" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return a subset of coordinate data for an AtomGroup</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>asel</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> object</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> object</p>
 </dd>
 <dt><em>start, stop, skip</em></dt>
 <dd><p class="first last">range of trajectory to access, start and stop are inclusive</p>
@@ -751,7 +777,7 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.DCD.DCDReader.totaltime">
-<tt class="descname">totaltime</tt><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.totaltime" title="Permalink to this definition">¶</a></dt>
+<code class="descname">totaltime</code><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDReader.totaltime" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total length of the trajectory n_frames * dt.</p>
 </dd></dl>
 
@@ -759,19 +785,20 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.DCD.</tt><tt class="descname">DCDWriter</tt><big>(</big><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>delta=20.45482949774598</em>, <em>dt=None</em>, <em>remarks=u'Created by DCDWriter'</em>, <em>convert_units=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.DCD.</code><code class="descname">DCDWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>delta=20.45482949774598</em>, <em>dt=None</em>, <em>remarks=u'Created by DCDWriter'</em>, <em>convert_units=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Writes to a DCD file</p>
 <p>Typical usage:</p>
-<div class="highlight-python"><pre>with DCDWriter("new.dcd", u.atoms.n_atoms) as w:
+<div class="highlight-python"><div class="highlight"><pre>with DCDWriter(&quot;new.dcd&quot;, u.atoms.n_atoms) as w:
     for ts in u.trajectory
-        w.write_next_timestep(ts)</pre>
+        w.write_next_timestep(ts)
+</pre></div>
 </div>
 <p>Keywords are available to set some of the low-level attributes of the DCD.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Methods :</th><td class="field-body"><tt class="docutils literal"><span class="pre">d</span> <span class="pre">=</span> <span class="pre">DCDWriter(dcdfilename,</span> <span class="pre">n_atoms,</span> <span class="pre">start,</span> <span class="pre">step,</span> <span class="pre">delta,</span> <span class="pre">remarks)</span></tt></td>
+<tr class="field-odd field"><th class="field-name">Methods:</th><td class="field-body"><code class="docutils literal"><span class="pre">d</span> <span class="pre">=</span> <span class="pre">DCDWriter(dcdfilename,</span> <span class="pre">n_atoms,</span> <span class="pre">start,</span> <span class="pre">step,</span> <span class="pre">delta,</span> <span class="pre">remarks)</span></code></td>
 </tr>
 </tbody>
 </table>
@@ -780,13 +807,13 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 <p>The Writer will write the <strong>unit cell information</strong> to the DCD in a
 format compatible with NAMD and older CHARMM versions, namely the unit
 cell lengths in Angstrom and the angle cosines (see
-<a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep" title="MDAnalysis.coordinates.DCD.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>). Newer versions of CHARMM (at least c36b2) store the
+<a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep" title="MDAnalysis.coordinates.DCD.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>). Newer versions of CHARMM (at least c36b2) store the
 matrix of the box vectors. Writing this matrix to a DCD is currently not
 supported (although reading is supported with the
-<a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDReader" title="MDAnalysis.coordinates.DCD.DCDReader"><tt class="xref py py-class docutils literal"><span class="pre">DCDReader</span></tt></a>); instead the angle cosines are written,
+<a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDReader" title="MDAnalysis.coordinates.DCD.DCDReader"><code class="xref py py-class docutils literal"><span class="pre">DCDReader</span></code></a>); instead the angle cosines are written,
 which <em>might make the DCD file unusable in CHARMM itself</em>. See
 <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/187">Issue 187</a> for further information.</p>
-<p class="last">The writing behavior of the <a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDWriter" title="MDAnalysis.coordinates.DCD.DCDWriter"><tt class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></tt></a> is identical to
+<p class="last">The writing behavior of the <a class="reference internal" href="#MDAnalysis.coordinates.DCD.DCDWriter" title="MDAnalysis.coordinates.DCD.DCDWriter"><code class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></code></a> is identical to
 that of the DCD molfile plugin of VMD with the exception that
 by default it will use AKMA time units.</p>
 </div>
@@ -819,13 +846,13 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </dd>
 <dt><em>dt</em></dt>
 <dd><p class="first last"><strong>Override</strong> <em>step</em> and <em>delta</em> so that the DCD records that <em>dt</em> ps
-lie between two frames. (It sets <em>step</em> = 1 and <em>delta</em> = <tt class="docutils literal"><span class="pre">AKMA(dt)</span></tt>.)
-The default is <tt class="docutils literal"><span class="pre">None</span></tt>, in which case <em>step</em> and <em>delta</em> are used.</p>
+lie between two frames. (It sets <em>step</em> = 1 and <em>delta</em> = <code class="docutils literal"><span class="pre">AKMA(dt)</span></code>.)
+The default is <code class="docutils literal"><span class="pre">None</span></code>, in which case <em>step</em> and <em>delta</em> are used.</p>
 </dd>
 <dt><em>convert_units</em></dt>
-<dd><p class="first last">units are converted to the MDAnalysis base format; <tt class="docutils literal"><span class="pre">None</span></tt> selects
-the value of <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> [&#8216;convert_lengths&#8217;].
-(see <a class="reference internal" href="../core/init.html#flags-label"><em>Flags</em></a>)</p>
+<dd><p class="first last">units are converted to the MDAnalysis base format; <code class="docutils literal"><span class="pre">None</span></code> selects
+the value of <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> [&#8216;convert_lengths&#8217;].
+(see <a class="reference internal" href="../core/init.html#flags-label"><span>Flags</span></a>)</p>
 </dd>
 </dl>
 </td>
@@ -843,114 +870,122 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDWriter.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDWriter.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close trajectory and flush buffers.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.convert_dimensions_to_unitcell">
-<tt class="descname">convert_dimensions_to_unitcell</tt><big>(</big><em>ts, _ts_order=[0, 2, 5, 4, 3, 1]</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDWriter.convert_dimensions_to_unitcell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_dimensions_to_unitcell</code><span class="sig-paren">(</span><em>ts, _ts_order=[0, 2, 5, 4, 3, 1]</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDWriter.convert_dimensions_to_unitcell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read dimensions from timestep <em>ts</em> and return appropriate native unitcell.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="MDAnalysis.coordinates.DCD.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep.dimensions" title="MDAnalysis.coordinates.DCD.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></code></a></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.has_valid_coordinates">
-<tt class="descname">has_valid_coordinates</tt><big>(</big><em>criteria</em>, <em>x</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns <tt class="docutils literal"><span class="pre">True</span></tt> if all values are within limit values of their formats.</p>
+<code class="descname">has_valid_coordinates</code><span class="sig-paren">(</span><em>criteria</em>, <em>x</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns <code class="docutils literal"><span class="pre">True</span></code> if all values are within limit values of their formats.</p>
 <p>Due to rounding, the test is asymmetric (and <em>min</em> is supposed to be negative):</p>
 <blockquote>
 <div>min &lt; x &lt;= max</div></blockquote>
@@ -958,17 +993,17 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>criteria</em></dt>
 <dd><p class="first last">dictionary containing the <em>max</em> and <em>min</em> values in native units</p>
 </dd>
 <dt><em>x</em></dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></tt> of <tt class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></tt> coordinates of atoms selected to be written out.</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></code> of <code class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></code> coordinates of atoms selected to be written out.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">boolean</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">boolean</p>
 </td>
 </tr>
 </tbody>
@@ -977,10 +1012,10 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.write">
-<tt class="descname">write</tt><big>(</big><em>obj</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write current timestep, using the supplied <em>obj</em>.</p>
-<p>The argument should be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> or
-a <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> or a <a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep" title="MDAnalysis.coordinates.DCD.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance.</p>
+<p>The argument should be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> or
+a <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> or a <a class="reference internal" href="#MDAnalysis.coordinates.DCD.Timestep" title="MDAnalysis.coordinates.DCD.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The size of the <em>obj</em> must be the same as the number of atom
@@ -990,13 +1025,14 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.DCD.DCDWriter.write_next_timestep">
-<tt class="descname">write_next_timestep</tt><big>(</big><em>ts=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDWriter.write_next_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_next_timestep</code><span class="sig-paren">(</span><em>ts=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDWriter.write_next_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DCD.DCDWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>write a new timestep to the dcd file</p>
 <p><em>ts</em> - timestep object containing coordinates to be written to dcd file</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Raises <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> instead of generic <tt class="xref py py-exc docutils literal"><span class="pre">Exception</span></tt>
-if wrong number of atoms supplied and <tt class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></tt>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Raises <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> instead of generic <code class="xref py py-exc docutils literal"><span class="pre">Exception</span></code>
+if wrong number of atoms supplied and <code class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></code>
 if no coordinates to be written.</p>
+</div>
 </dd></dl>
 
 </dd></dl>
@@ -1010,7 +1046,7 @@ <h2>5.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1025,11 +1061,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="CRD.html" title="5.2. CRD structure files in MDAnalysis — MDAnalysis.coordinates.CRD"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -1039,7 +1075,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/DLPoly.html b/package/doc/html/documentation_pages/coordinates/DLPoly.html
index 4f24852d47d..c39bfe5fa3f 100644
--- a/package/doc/html/documentation_pages/coordinates/DLPoly.html
+++ b/package/doc/html/documentation_pages/coordinates/DLPoly.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.5. DESRES file format — MDAnalysis.coordinates.DMS" href="DMS.html" />
     <link rel="prev" title="5.3. DCD trajectory I/O — MDAnalysis.coordinates.DCD" href="DCD.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="DCD.html" title="5.3. DCD trajectory I/O — MDAnalysis.coordinates.DCD"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="DCD.html"
-                        title="previous chapter">5.3. DCD trajectory I/O  &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></tt></a></p>
+                        title="previous chapter">5.3. DCD trajectory I/O  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="DMS.html"
-                        title="next chapter">5.5. DESRES file format &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.DMS</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/DLPoly.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.5. DESRES file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.DMS</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/DLPoly.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,25 +90,27 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.DLPoly"></span><div class="section" id="dl-poly-format-reader-mdanalysis-coordinates-dlpoly">
-<h1>5.4. DL_Poly format reader <a class="reference internal" href="#module-MDAnalysis.coordinates.DLPoly" title="MDAnalysis.coordinates.DLPoly"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DLPoly</span></tt></a><a class="headerlink" href="#dl-poly-format-reader-mdanalysis-coordinates-dlpoly" title="Permalink to this headline">¶</a></h1>
+<h1>5.4. DL_Poly format reader <a class="reference internal" href="#module-MDAnalysis.coordinates.DLPoly" title="MDAnalysis.coordinates.DLPoly"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DLPoly</span></code></a><a class="headerlink" href="#dl-poly-format-reader-mdanalysis-coordinates-dlpoly" title="Permalink to this headline">¶</a></h1>
 <p>Read DL <a class="reference external" href="http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/44516.aspx">Poly</a> format coordinate files</p>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.DLPoly.ConfigReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.DLPoly.</tt><tt class="descname">ConfigReader</tt><big>(</big><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DLPoly.html#ConfigReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DLPoly.ConfigReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.DLPoly.</code><code class="descname">ConfigReader</code><span class="sig-paren">(</span><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DLPoly.html#ConfigReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DLPoly.ConfigReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>DLPoly Config file Reader</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.DLPoly.HistoryReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.DLPoly.</tt><tt class="descname">HistoryReader</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DLPoly.html#HistoryReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DLPoly.HistoryReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.DLPoly.</code><code class="descname">HistoryReader</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DLPoly.html#HistoryReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DLPoly.HistoryReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reads DLPoly format HISTORY files</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 </div>
@@ -119,7 +121,7 @@ <h1>5.4. DL_Poly format reader <a class="reference internal" href="#module-MDAna
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -134,11 +136,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="DCD.html" title="5.3. DCD trajectory I/O — MDAnalysis.coordinates.DCD"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -148,7 +150,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/DMS.html b/package/doc/html/documentation_pages/coordinates/DMS.html
index e2fb289a89e..a49bcb2c00d 100644
--- a/package/doc/html/documentation_pages/coordinates/DMS.html
+++ b/package/doc/html/documentation_pages/coordinates/DMS.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.5. DESRES file format — MDAnalysis.coordinates.DMS &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.5. DESRES file format — MDAnalysis.coordinates.DMS &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.6. GAMESS trajectory reader — MDAnalysis.coordinates.GMS" href="GMS.html" />
     <link rel="prev" title="5.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly" href="DLPoly.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="DLPoly.html" title="5.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="DLPoly.html"
-                        title="previous chapter">5.4. DL_Poly format reader <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.DLPoly</span></tt></a></p>
+                        title="previous chapter">5.4. DL_Poly format reader <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.DLPoly</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="GMS.html"
-                        title="next chapter">5.6. GAMESS trajectory reader &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.GMS</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/DMS.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.6. GAMESS trajectory reader &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.GMS</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/DMS.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,18 +90,19 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.DMS"></span><div class="section" id="desres-file-format-mdanalysis-coordinates-dms">
-<h1>5.5. DESRES file format &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.DMS" title="MDAnalysis.coordinates.DMS"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DMS</span></tt></a><a class="headerlink" href="#desres-file-format-mdanalysis-coordinates-dms" title="Permalink to this headline">¶</a></h1>
+<h1>5.5. DESRES file format &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.DMS" title="MDAnalysis.coordinates.DMS"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DMS</span></code></a><a class="headerlink" href="#desres-file-format-mdanalysis-coordinates-dms" title="Permalink to this headline">¶</a></h1>
 <p>Classes to read <a class="reference external" href="http://www.deshawresearch.com">DESRES</a> Molecular Structure file format (<a class="reference external" href="http://www.deshawresearch.com/Desmond_Users_Guide-0.7.pdf">DMS</a>)
 coordinate files (as used by the <a class="reference external" href="http://www.deshawresearch.com/resources_desmond.html">Desmond</a> MD package).</p>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.DMS.DMSReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.DMS.</tt><tt class="descname">DMSReader</tt><big>(</big><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DMS.html#DMSReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DMS.DMSReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.DMS.</code><code class="descname">DMSReader</code><span class="sig-paren">(</span><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DMS.html#DMSReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.DMS.DMSReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reads both coordinates and velocities.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 </dd></dl>
 
 </div>
@@ -112,7 +113,7 @@ <h1>5.5. DESRES file format &#8212; <a class="reference internal" href="#module-
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -127,11 +128,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="DLPoly.html" title="5.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -141,7 +142,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/GMS.html b/package/doc/html/documentation_pages/coordinates/GMS.html
index b9f6f7bdfc7..acdad4a5133 100644
--- a/package/doc/html/documentation_pages/coordinates/GMS.html
+++ b/package/doc/html/documentation_pages/coordinates/GMS.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.6. GAMESS trajectory reader — MDAnalysis.coordinates.GMS &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.6. GAMESS trajectory reader — MDAnalysis.coordinates.GMS &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.7. GRO file format — MDAnalysis.coordinates.GRO" href="GRO.html" />
     <link rel="prev" title="5.5. DESRES file format — MDAnalysis.coordinates.DMS" href="DMS.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="DMS.html" title="5.5. DESRES file format — MDAnalysis.coordinates.DMS"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="DMS.html"
-                        title="previous chapter">5.5. DESRES file format &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.DMS</span></tt></a></p>
+                        title="previous chapter">5.5. DESRES file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.DMS</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="GRO.html"
-                        title="next chapter">5.7. GRO file format &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/GMS.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.7. GRO file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/GMS.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,10 +90,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.GMS"></span><div class="section" id="gamess-trajectory-reader-mdanalysis-coordinates-gms">
-<h1>5.6. GAMESS trajectory reader &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.GMS" title="MDAnalysis.coordinates.GMS"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.GMS</span></tt></a><a class="headerlink" href="#gamess-trajectory-reader-mdanalysis-coordinates-gms" title="Permalink to this headline">¶</a></h1>
+<h1>5.6. GAMESS trajectory reader &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.GMS" title="MDAnalysis.coordinates.GMS"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.GMS</span></code></a><a class="headerlink" href="#gamess-trajectory-reader-mdanalysis-coordinates-gms" title="Permalink to this headline">¶</a></h1>
 <p>Resources: the GMS output format is a common output format for different
 GAMESS distributions: US-GAMESS, Firefly (PC-GAMESS) and GAMESS-UK.</p>
 <p>Current version was approbated with US-GAMESS &amp; Firefly only.</p>
@@ -107,7 +107,7 @@ <h1>5.6. GAMESS trajectory reader &#8212; <a class="reference internal" href="#m
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -122,11 +122,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="DMS.html" title="5.5. DESRES file format — MDAnalysis.coordinates.DMS"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -136,7 +136,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/GRO.html b/package/doc/html/documentation_pages/coordinates/GRO.html
index e2f953199da..e9f0d00c7b8 100644
--- a/package/doc/html/documentation_pages/coordinates/GRO.html
+++ b/package/doc/html/documentation_pages/coordinates/GRO.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.7. GRO file format — MDAnalysis.coordinates.GRO &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.7. GRO file format — MDAnalysis.coordinates.GRO &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.8. INPCRD structure files in MDAnalysis — MDAnalysis.coordinates.INPCRD" href="INPCRD.html" />
     <link rel="prev" title="5.6. GAMESS trajectory reader — MDAnalysis.coordinates.GMS" href="GMS.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="GMS.html" title="5.6. GAMESS trajectory reader — MDAnalysis.coordinates.GMS"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="GMS.html"
-                        title="previous chapter">5.6. GAMESS trajectory reader &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.GMS</span></tt></a></p>
+                        title="previous chapter">5.6. GAMESS trajectory reader &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.GMS</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="INPCRD.html"
-                        title="next chapter">5.8. INPCRD structure files in MDAnalysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.INPCRD</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/GRO.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.8. INPCRD structure files in MDAnalysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.INPCRD</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/GRO.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,34 +90,35 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.GRO"></span><div class="section" id="gro-file-format-mdanalysis-coordinates-gro">
-<h1>5.7. GRO file format &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.GRO" title="MDAnalysis.coordinates.GRO"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></tt></a><a class="headerlink" href="#gro-file-format-mdanalysis-coordinates-gro" title="Permalink to this headline">¶</a></h1>
+<h1>5.7. GRO file format &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.GRO" title="MDAnalysis.coordinates.GRO"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></code></a><a class="headerlink" href="#gro-file-format-mdanalysis-coordinates-gro" title="Permalink to this headline">¶</a></h1>
 <p>Classes to read and write <a class="reference external" href="http://www.gromacs.org">Gromacs</a> <a class="reference external" href="http://manual.gromacs.org/current/online/gro.html">GRO</a> coordinate files; see the notes on the
 <a class="reference external" href="http://chembytes.wikidot.com/g-grofile">GRO format</a> which includes a conversion routine for the box.</p>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.GRO.GROReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.GRO.</tt><tt class="descname">GROReader</tt><big>(</big><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GRO.html#GROReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.GRO.</code><code class="descname">GROReader</code><span class="sig-paren">(</span><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GRO.html#GROReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reader for the Gromacs GRO structure format.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.GRO.GROReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GRO.html#GROReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GRO.html#GROReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a CRDWriter for <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output GRO file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.GRO.GROWriter" title="MDAnalysis.coordinates.GRO.GROWriter"><tt class="xref py py-class docutils literal"><span class="pre">GROWriter</span></tt></a></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.GRO.GROWriter" title="MDAnalysis.coordinates.GRO.GROWriter"><code class="xref py py-class docutils literal"><span class="pre">GROWriter</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -128,21 +129,22 @@ <h1>5.7. GRO file format &#8212; <a class="reference internal" href="#module-MDA
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.GRO.GROWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.GRO.</tt><tt class="descname">GROWriter</tt><big>(</big><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GRO.html#GROWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.GRO.</code><code class="descname">GROWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GRO.html#GROWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>GRO Writer that conforms to the Trajectory API.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The precision is hard coded to three decimal places and
 velocities are not written (yet).</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 <p>Set up a GROWriter with a precision of 3 decimal places.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">output filename</p>
 </dd>
@@ -153,26 +155,26 @@ <h1>5.7. GRO file format &#8212; <a class="reference internal" href="#module-MDA
 </table>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.GRO.GROWriter.convert_dimensions_to_unitcell">
-<tt class="descname">convert_dimensions_to_unitcell</tt><big>(</big><em>ts</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GRO.html#GROWriter.convert_dimensions_to_unitcell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_dimensions_to_unitcell</code><span class="sig-paren">(</span><em>ts</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GRO.html#GROWriter.convert_dimensions_to_unitcell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read dimensions from timestep <em>ts</em> and return appropriate unitcell</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.GRO.GROWriter.fmt">
-<tt class="descname">fmt</tt><em class="property"> = {'box_orthorhombic': '%10.5f%10.5f%10.5f\n', 'box_triclinic': '%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f\n', 'n_atoms': '%5d\n', 'xyz': '%5s%-5s%5s%5s%8.3f%8.3f%8.3f\n', 'xyz_v': '%5s%-5s%5s%5s%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f\n'}</em><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROWriter.fmt" title="Permalink to this definition">¶</a></dt>
+<code class="descname">fmt</code><em class="property"> = {'box_orthorhombic': '%10.5f%10.5f%10.5f\n', 'box_triclinic': '%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f\n', 'n_atoms': '%5d\n', 'xyz': '%5s%-5s%5s%5s%8.3f%8.3f%8.3f\n', 'xyz_v': '%5s%-5s%5s%5s%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f\n'}</em><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROWriter.fmt" title="Permalink to this definition">¶</a></dt>
 <dd><p>format strings for the GRO file (all include newline); precision
 of 3 decimal places is hard-coded here.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.GRO.GROWriter.write">
-<tt class="descname">write</tt><big>(</big><em>selection</em>, <em>frame=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GRO.html#GROWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>selection</em>, <em>frame=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GRO.html#GROWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.GRO.GROWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write selection at current trajectory frame to file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt>selection</dt>
 <dd><p class="first last">MDAnalysis AtomGroup (selection or Universe.atoms)
 or also Universe</p>
@@ -180,7 +182,7 @@ <h1>5.7. GRO file format &#8212; <a class="reference internal" href="#module-MDA
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt>frame</dt>
 <dd><p class="first last">optionally move to frame number <em>frame</em></p>
 </dd>
@@ -192,8 +194,9 @@ <h1>5.7. GRO file format &#8212; <a class="reference internal" href="#module-MDA
 <p>The GRO format only allows 5 digits for resid and atom
 number. If these number become larger than 99,999 then this
 routine will chop off the leading digits.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>resName and atomName are truncated to a maximum of 5 characters</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>resName and atomName are truncated to a maximum of 5 characters</p>
+</div>
 </dd></dl>
 
 </dd></dl>
@@ -206,7 +209,7 @@ <h1>5.7. GRO file format &#8212; <a class="reference internal" href="#module-MDA
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -221,11 +224,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="GMS.html" title="5.6. GAMESS trajectory reader — MDAnalysis.coordinates.GMS"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -235,7 +238,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/INPCRD.html b/package/doc/html/documentation_pages/coordinates/INPCRD.html
index 63d0c7fc475..97e112d6d61 100644
--- a/package/doc/html/documentation_pages/coordinates/INPCRD.html
+++ b/package/doc/html/documentation_pages/coordinates/INPCRD.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.8. INPCRD structure files in MDAnalysis — MDAnalysis.coordinates.INPCRD &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.8. INPCRD structure files in MDAnalysis — MDAnalysis.coordinates.INPCRD &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.9. LAMMPS DCD trajectory I/O — MDAnalysis.coordinates.LAMMPS" href="LAMMPS.html" />
     <link rel="prev" title="5.7. GRO file format — MDAnalysis.coordinates.GRO" href="GRO.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="GRO.html" title="5.7. GRO file format — MDAnalysis.coordinates.GRO"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="GRO.html"
-                        title="previous chapter">5.7. GRO file format &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></tt></a></p>
+                        title="previous chapter">5.7. GRO file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="LAMMPS.html"
-                        title="next chapter">5.9. LAMMPS DCD trajectory I/O  &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/INPCRD.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.9. LAMMPS DCD trajectory I/O  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/INPCRD.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,10 +90,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.INPCRD"></span><div class="section" id="inpcrd-structure-files-in-mdanalysis-mdanalysis-coordinates-inpcrd">
-<h1>5.8. INPCRD structure files in MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.INPCRD" title="MDAnalysis.coordinates.INPCRD"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.INPCRD</span></tt></a><a class="headerlink" href="#inpcrd-structure-files-in-mdanalysis-mdanalysis-coordinates-inpcrd" title="Permalink to this headline">¶</a></h1>
+<h1>5.8. INPCRD structure files in MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.INPCRD" title="MDAnalysis.coordinates.INPCRD"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.INPCRD</span></code></a><a class="headerlink" href="#inpcrd-structure-files-in-mdanalysis-mdanalysis-coordinates-inpcrd" title="Permalink to this headline">¶</a></h1>
 <p>Read and write coordinates in <a class="reference external" href="http://ambermd.org/formats.html#restart">Amber</a> coordinate/restart file (suffix
 &#8220;inpcrd&#8221;).</p>
 </div>
@@ -104,7 +104,7 @@ <h1>5.8. INPCRD structure files in MDAnalysis &#8212; <a class="reference intern
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -119,11 +119,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="GRO.html" title="5.7. GRO file format — MDAnalysis.coordinates.GRO"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -133,7 +133,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/LAMMPS.html b/package/doc/html/documentation_pages/coordinates/LAMMPS.html
index 532b14d54fb..328ab7a791c 100644
--- a/package/doc/html/documentation_pages/coordinates/LAMMPS.html
+++ b/package/doc/html/documentation_pages/coordinates/LAMMPS.html
@@ -1,5 +1,3 @@
-
-
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-<li><a class="reference internal" href="#">5.9. LAMMPS DCD trajectory I/O  &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.9. LAMMPS DCD trajectory I/O  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></code></a><ul>
 <li><a class="reference internal" href="#classes">5.9.1. Classes</a></li>
 </ul>
 </li>
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   <span class="target" id="module-MDAnalysis.coordinates.LAMMPS"></span><div class="section" id="lammps-dcd-trajectory-i-o-mdanalysis-coordinates-lammps">
-<h1>5.9. LAMMPS DCD trajectory I/O  &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.LAMMPS" title="MDAnalysis.coordinates.LAMMPS"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></tt></a><a class="headerlink" href="#lammps-dcd-trajectory-i-o-mdanalysis-coordinates-lammps" title="Permalink to this headline">¶</a></h1>
+<h1>5.9. LAMMPS DCD trajectory I/O  &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.LAMMPS" title="MDAnalysis.coordinates.LAMMPS"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></code></a><a class="headerlink" href="#lammps-dcd-trajectory-i-o-mdanalysis-coordinates-lammps" title="Permalink to this headline">¶</a></h1>
 <p>Classes to read and write <a class="reference external" href="http://lammps.sandia.gov/">LAMMPS</a> DCD binary
 trajectories. Trajectories can be read regardless of system-endianness
 as this is auto-detected.</p>
@@ -116,14 +116,14 @@ <h1>5.9. LAMMPS DCD trajectory I/O  &#8212; <a class="reference internal" href="
 the unit from the file. By default we are assuming that the unit for
 length is the ångström and for the time is the picosecond. If this is
 not true then the user <em>should supply the appropriate units</em> in the as
-keywords <em>timeunit</em> and/or <em>lengthunit</em> to <a class="reference internal" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter" title="MDAnalysis.coordinates.LAMMPS.DCDWriter"><tt class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></tt></a> and
-<a class="reference internal" href="#MDAnalysis.coordinates.LAMMPS.DCDReader" title="MDAnalysis.coordinates.LAMMPS.DCDReader"><tt class="xref py py-class docutils literal"><span class="pre">DCDReader</span></tt></a>.</p>
+keywords <em>timeunit</em> and/or <em>lengthunit</em> to <a class="reference internal" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter" title="MDAnalysis.coordinates.LAMMPS.DCDWriter"><code class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></code></a> and
+<a class="reference internal" href="#MDAnalysis.coordinates.LAMMPS.DCDReader" title="MDAnalysis.coordinates.LAMMPS.DCDReader"><code class="xref py py-class docutils literal"><span class="pre">DCDReader</span></code></a>.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">Lennard-Jones units are not implemented. See
-<a class="reference internal" href="../units.html#module-MDAnalysis.units" title="MDAnalysis.units"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.units</span></tt></a> for other recognized values.</p>
+<a class="reference internal" href="../units.html#module-MDAnalysis.units" title="MDAnalysis.units"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.units</span></code></a> for other recognized values.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">For further discussion follow the reports for <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/84">Issue 84</a> and <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/64">Issue 64</a>.</p>
 </div>
@@ -131,41 +131,41 @@ <h1>5.9. LAMMPS DCD trajectory I/O  &#8212; <a class="reference internal" href="
 <h2>5.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.LAMMPS.</tt><tt class="descname">DCDReader</tt><big>(</big><em>dcdfilename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/LAMMPS.html#DCDReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.LAMMPS.</code><code class="descname">DCDReader</code><span class="sig-paren">(</span><em>dcdfilename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/LAMMPS.html#DCDReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read a <a class="reference external" href="http://lammps.sandia.gov/">LAMMPS</a> DCD trajectory.</p>
 <p>The units can be set from the constructor with the keyword
 arguments <em>timeunit</em> and <em>lengthunit</em>. The defaults are &#8220;ps&#8221; and
-&#8220;Angstrom&#8221;. See <a class="reference internal" href="../units.html#module-MDAnalysis.units" title="MDAnalysis.units"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.units</span></tt></a> for other recognized
+&#8220;Angstrom&#8221;. See <a class="reference internal" href="../units.html#module-MDAnalysis.units" title="MDAnalysis.units"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.units</span></code></a> for other recognized
 values.</p>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.OtherWriter">
-<tt class="descname">OtherWriter</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">OtherWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a writer appropriate for <em>filename</em>.</p>
 <p>Sets the default keywords <em>start</em>, <em>step</em> and <em>dt</em> (if
-available). <em>n_atoms</em> is always set from <tt class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></tt>.</p>
-<div class="admonition-see-also admonition seealso">
+available). <em>n_atoms</em> is always set from <code class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></code>.</p>
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></tt> and <tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></tt></p>
+<p class="last"><code class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></code> and <code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a DCDWriter for <em>filename</em> with the same parameters as this DCD.</p>
 <p>All values can be changed through keyword arguments.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output DCD trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">number of atoms</p>
 </dd>
@@ -180,8 +180,8 @@ <h2>5.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </dd>
 <dt><em>dt</em></dt>
 <dd><p class="first last"><strong>Override</strong> <em>step</em> and <em>delta</em> so that the DCD records that <em>dt</em> ps
-lie between two frames. (It sets <em>step</em> = 1 and <em>delta</em> = <tt class="docutils literal"><span class="pre">AKMA(dt)</span></tt>.)
-The default is <tt class="docutils literal"><span class="pre">None</span></tt>, in which case <em>step</em> and <em>delta</em> are used.</p>
+lie between two frames. (It sets <em>step</em> = 1 and <em>delta</em> = <code class="docutils literal"><span class="pre">AKMA(dt)</span></code>.)
+The default is <code class="docutils literal"><span class="pre">None</span></code>, in which case <em>step</em> and <em>delta</em> are used.</p>
 </dd>
 <dt><em>remarks</em></dt>
 <dd><p class="first last">string that is stored in the DCD header [XXX &#8211; max length?]</p>
@@ -189,7 +189,7 @@ <h2>5.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter" title="MDAnalysis.coordinates.LAMMPS.DCDWriter"><tt class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></tt></a></p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter" title="MDAnalysis.coordinates.LAMMPS.DCDWriter"><code class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -200,113 +200,121 @@ <h2>5.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 according to the CHARMM format. The time between two frames would be
 <em>delta</em> * <em>step</em> !</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter" title="MDAnalysis.coordinates.LAMMPS.DCDWriter"><tt class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></tt></a> has detailed argument description</p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter" title="MDAnalysis.coordinates.LAMMPS.DCDWriter"><code class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></code></a> has detailed argument description</p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.correl">
-<tt class="descname">correl</tt><big>(</big><em>timeseries</em>, <em>start=0</em>, <em>stop=-1</em>, <em>skip=1</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.correl" title="Permalink to this definition">¶</a></dt>
+<code class="descname">correl</code><span class="sig-paren">(</span><em>timeseries</em>, <em>start=0</em>, <em>stop=-1</em>, <em>skip=1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDReader.correl"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.correl" title="Permalink to this definition">¶</a></dt>
 <dd><p>Populate a TimeseriesCollection object with timeseries computed from the trajectory</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>timeseries</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/Timeseries.html#MDAnalysis.core.Timeseries.TimeseriesCollection" title="MDAnalysis.core.Timeseries.TimeseriesCollection"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.Timeseries.TimeseriesCollection</span></tt></a></p>
+<dd><p class="first last"><a class="reference internal" href="../core/Timeseries.html#MDAnalysis.core.Timeseries.TimeseriesCollection" title="MDAnalysis.core.Timeseries.TimeseriesCollection"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.Timeseries.TimeseriesCollection</span></code></a></p>
 </dd>
 <dt><em>start, stop, skip</em></dt>
 <dd><p class="first last">subset of trajectory to use, with start and stop being inclusive</p>
@@ -320,42 +328,42 @@ <h2>5.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.frame">
-<tt class="descname">frame</tt><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.frame" title="Permalink to this definition">¶</a></dt>
+<code class="descname">frame</code><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.frame" title="Permalink to this definition">¶</a></dt>
 <dd><p>Frame number of the current time step.</p>
-<p>This is a simple short cut to <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt>.</p>
+<p>This is a simple short cut to <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.next">
-<tt class="descname">next</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.next" title="Permalink to this definition">¶</a></dt>
+<code class="descname">next</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.next" title="Permalink to this definition">¶</a></dt>
 <dd><p>Forward one step to next frame.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.rewind">
-<tt class="descname">rewind</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.rewind" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rewind</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.rewind" title="Permalink to this definition">¶</a></dt>
 <dd><p>Position at beginning of trajectory</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>Time of the current frame in MDAnalysis time units (typically ps).</p>
 <p>This is either read straight from the Timestep, or calculated as
-time = <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt> * <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></tt></p>
+time = <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code> * <code class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></code></p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.timeseries">
-<tt class="descname">timeseries</tt><big>(</big><em>asel</em>, <em>start=0</em>, <em>stop=-1</em>, <em>skip=1</em>, <em>format=u'afc'</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.timeseries" title="Permalink to this definition">¶</a></dt>
+<code class="descname">timeseries</code><span class="sig-paren">(</span><em>asel</em>, <em>start=0</em>, <em>stop=-1</em>, <em>skip=1</em>, <em>format=u'afc'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDReader.timeseries"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.timeseries" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return a subset of coordinate data for an AtomGroup</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>asel</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> object</p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> object</p>
 </dd>
 <dt><em>start, stop, skip</em></dt>
 <dd><p class="first last">range of trajectory to access, start and stop are inclusive</p>
@@ -376,7 +384,7 @@ <h2>5.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDReader.totaltime">
-<tt class="descname">totaltime</tt><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.totaltime" title="Permalink to this definition">¶</a></dt>
+<code class="descname">totaltime</code><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDReader.totaltime" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total length of the trajectory n_frames * dt.</p>
 </dd></dl>
 
@@ -384,122 +392,130 @@ <h2>5.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.LAMMPS.</tt><tt class="descname">DCDWriter</tt><big>(</big><em>*args</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/LAMMPS.html#DCDWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.LAMMPS.</code><code class="descname">DCDWriter</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/LAMMPS.html#DCDWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a <a class="reference external" href="http://lammps.sandia.gov/">LAMMPS</a> DCD trajectory.</p>
 <p>The units can be set from the constructor with the keyword
 arguments <em>timeunit</em> and <em>lengthunit</em>. The defaults are &#8220;ps&#8221; and
-&#8220;Angstrom&#8221;. See <a class="reference internal" href="../units.html#module-MDAnalysis.units" title="MDAnalysis.units"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.units</span></tt></a> for other recognized
+&#8220;Angstrom&#8221;. See <a class="reference internal" href="../units.html#module-MDAnalysis.units" title="MDAnalysis.units"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.units</span></code></a> for other recognized
 values.</p>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDWriter.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close trajectory and flush buffers.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_dimensions_to_unitcell">
-<tt class="descname">convert_dimensions_to_unitcell</tt><big>(</big><em>ts, _ts_order=[0, 2, 5, 4, 3, 1]</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_dimensions_to_unitcell</code><span class="sig-paren">(</span><em>ts, _ts_order=[0, 2, 5, 4, 3, 1]</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDWriter.convert_dimensions_to_unitcell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read dimensions from timestep <em>ts</em> and return appropriate native unitcell.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></tt></p>
+<p class="last"><code class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.has_valid_coordinates">
-<tt class="descname">has_valid_coordinates</tt><big>(</big><em>criteria</em>, <em>x</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns <tt class="docutils literal"><span class="pre">True</span></tt> if all values are within limit values of their formats.</p>
+<code class="descname">has_valid_coordinates</code><span class="sig-paren">(</span><em>criteria</em>, <em>x</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns <code class="docutils literal"><span class="pre">True</span></code> if all values are within limit values of their formats.</p>
 <p>Due to rounding, the test is asymmetric (and <em>min</em> is supposed to be negative):</p>
 <blockquote>
 <div>min &lt; x &lt;= max</div></blockquote>
@@ -507,17 +523,17 @@ <h2>5.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>criteria</em></dt>
 <dd><p class="first last">dictionary containing the <em>max</em> and <em>min</em> values in native units</p>
 </dd>
 <dt><em>x</em></dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></tt> of <tt class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></tt> coordinates of atoms selected to be written out.</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></code> of <code class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></code> coordinates of atoms selected to be written out.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">boolean</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">boolean</p>
 </td>
 </tr>
 </tbody>
@@ -526,10 +542,10 @@ <h2>5.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.write">
-<tt class="descname">write</tt><big>(</big><em>obj</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write current timestep, using the supplied <em>obj</em>.</p>
-<p>The argument should be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> or
-a <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> or a <tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt> instance.</p>
+<p>The argument should be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> or
+a <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> or a <code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code> instance.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The size of the <em>obj</em> must be the same as the number of atom
@@ -539,157 +555,168 @@ <h2>5.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DCDWriter.write_next_timestep">
-<tt class="descname">write_next_timestep</tt><big>(</big><em>ts=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_next_timestep</code><span class="sig-paren">(</span><em>ts=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/DCD.html#DCDWriter.write_next_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DCDWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>write a new timestep to the dcd file</p>
 <p><em>ts</em> - timestep object containing coordinates to be written to dcd file</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Raises <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> instead of generic <tt class="xref py py-exc docutils literal"><span class="pre">Exception</span></tt>
-if wrong number of atoms supplied and <tt class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></tt>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Raises <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> instead of generic <code class="xref py py-exc docutils literal"><span class="pre">Exception</span></code>
+if wrong number of atoms supplied and <code class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></code>
 if no coordinates to be written.</p>
+</div>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.LAMMPS.</tt><tt class="descname">DATAReader</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/LAMMPS.html#DATAReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.LAMMPS.</code><code class="descname">DATAReader</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/LAMMPS.html#DATAReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reads a single frame of coordinate information from a LAMMPS DATA file.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.OtherWriter">
-<tt class="descname">OtherWriter</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">OtherWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a writer appropriate for <em>filename</em>.</p>
 <p>Sets the default keywords <em>start</em>, <em>step</em> and <em>dt</em> (if
-available). <em>n_atoms</em> is always set from <tt class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></tt>.</p>
-<div class="admonition-see-also admonition seealso">
+available). <em>n_atoms</em> is always set from <code class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></code>.</p>
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></tt> and <tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></tt></p>
+<p class="last"><code class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></code> and <code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a trajectory writer with the same properties as this trajectory.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.dt" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dt</code><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.dt" title="Permalink to this definition">¶</a></dt>
 <dd><p>Time between two trajectory frames in picoseconds.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.frame">
-<tt class="descname">frame</tt><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.frame" title="Permalink to this definition">¶</a></dt>
+<code class="descname">frame</code><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.frame" title="Permalink to this definition">¶</a></dt>
 <dd><p>Frame number of the current time step.</p>
-<p>This is a simple short cut to <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt>.</p>
+<p>This is a simple short cut to <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code>.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>Time of the current frame in MDAnalysis time units (typically ps).</p>
 <p>This is either read straight from the Timestep, or calculated as
-time = <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt> * <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></tt></p>
+time = <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code> * <code class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></code></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.LAMMPS.DATAReader.totaltime">
-<tt class="descname">totaltime</tt><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.totaltime" title="Permalink to this definition">¶</a></dt>
+<code class="descname">totaltime</code><a class="headerlink" href="#MDAnalysis.coordinates.LAMMPS.DATAReader.totaltime" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total length of the trajectory n_frames * dt.</p>
 </dd></dl>
 
@@ -704,7 +731,7 @@ <h2>5.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -719,11 +746,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="INPCRD.html" title="5.8. INPCRD structure files in MDAnalysis — MDAnalysis.coordinates.INPCRD"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -733,7 +760,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/MOL2.html b/package/doc/html/documentation_pages/coordinates/MOL2.html
index fe625fd658d..b976d1f5109 100644
--- a/package/doc/html/documentation_pages/coordinates/MOL2.html
+++ b/package/doc/html/documentation_pages/coordinates/MOL2.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.10. MOL2 file format — MDAnalysis.coordinates.MOL2 &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.10. MOL2 file format — MDAnalysis.coordinates.MOL2 &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.11. PDB structure files in MDAnalysis — MDAnalysis.coordinates.PDB" href="PDB.html" />
     <link rel="prev" title="5.9. LAMMPS DCD trajectory I/O — MDAnalysis.coordinates.LAMMPS" href="LAMMPS.html" /> 
   </head>
-  <body>
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="LAMMPS.html" title="5.9. LAMMPS DCD trajectory I/O — MDAnalysis.coordinates.LAMMPS"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.10. MOL2 file format &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.10. MOL2 file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></code></a><ul>
 <li><a class="reference internal" href="#examples">5.10.1. Examples</a></li>
 </ul>
 </li>
@@ -70,16 +68,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="LAMMPS.html"
-                        title="previous chapter">5.9. LAMMPS DCD trajectory I/O  &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></tt></a></p>
+                        title="previous chapter">5.9. LAMMPS DCD trajectory I/O  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="PDB.html"
-                        title="next chapter">5.11. PDB structure files in MDAnalysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/MOL2.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.11. PDB structure files in MDAnalysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/MOL2.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,10 +98,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.MOL2"></span><div class="section" id="mol2-file-format-mdanalysis-coordinates-mol2">
-<h1>5.10. MOL2 file format &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.MOL2" title="MDAnalysis.coordinates.MOL2"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></tt></a><a class="headerlink" href="#mol2-file-format-mdanalysis-coordinates-mol2" title="Permalink to this headline">¶</a></h1>
+<h1>5.10. MOL2 file format &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.MOL2" title="MDAnalysis.coordinates.MOL2"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></code></a><a class="headerlink" href="#mol2-file-format-mdanalysis-coordinates-mol2" title="Permalink to this headline">¶</a></h1>
 <p>Classes to read <a class="reference external" href="http://www.tripos.com/">Tripos</a> molecule structure format (<a class="reference external" href="http://www.tripos.com/data/support/mol2.pdf">MOL2</a>)
 coordinate and topology files. Used by the <a class="reference external" href="http://dock.compbio.ucsf.edu/">DOCK</a> docking
 code.</p>
@@ -123,7 +123,7 @@ <h2>5.10.1. Examples<a class="headerlink" href="#examples" title="Permalink to t
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -138,11 +138,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="LAMMPS.html" title="5.9. LAMMPS DCD trajectory I/O — MDAnalysis.coordinates.LAMMPS"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -152,7 +152,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/PDB.html b/package/doc/html/documentation_pages/coordinates/PDB.html
index f14536f4733..46225bf95d5 100644
--- a/package/doc/html/documentation_pages/coordinates/PDB.html
+++ b/package/doc/html/documentation_pages/coordinates/PDB.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.11. PDB structure files in MDAnalysis — MDAnalysis.coordinates.PDB &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.11. PDB structure files in MDAnalysis — MDAnalysis.coordinates.PDB &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
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@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.12. PDBQT structure files in MDAnalysis — MDAnalysis.coordinates.PDBQT" href="PDBQT.html" />
     <link rel="prev" title="5.10. MOL2 file format — MDAnalysis.coordinates.MOL2" href="MOL2.html" /> 
   </head>
-  <body>
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="MOL2.html" title="5.10. MOL2 file format — MDAnalysis.coordinates.MOL2"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.11. PDB structure files in MDAnalysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.11. PDB structure files in MDAnalysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></code></a><ul>
 <li><a class="reference internal" href="#implementations">5.11.1. Implementations</a></li>
 <li><a class="reference internal" href="#simple-permissive-pdb-reader-and-writer">5.11.2. Simple (permissive) PDB Reader and Writer</a><ul>
 <li><a class="reference internal" href="#examples">5.11.2.1. Examples</a></li>
@@ -80,16 +78,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="MOL2.html"
-                        title="previous chapter">5.10. MOL2 file format &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></tt></a></p>
+                        title="previous chapter">5.10. MOL2 file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="PDBQT.html"
-                        title="next chapter">5.12. PDBQT structure files in MDAnalysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.PDBQT</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/PDB.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.12. PDBQT structure files in MDAnalysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.PDBQT</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/PDB.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -108,10 +108,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.PDB"></span><div class="section" id="pdb-structure-files-in-mdanalysis-mdanalysis-coordinates-pdb">
-<h1>5.11. PDB structure files in MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.PDB" title="MDAnalysis.coordinates.PDB"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></tt></a><a class="headerlink" href="#pdb-structure-files-in-mdanalysis-mdanalysis-coordinates-pdb" title="Permalink to this headline">¶</a></h1>
+<h1>5.11. PDB structure files in MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.PDB" title="MDAnalysis.coordinates.PDB"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></code></a><a class="headerlink" href="#pdb-structure-files-in-mdanalysis-mdanalysis-coordinates-pdb" title="Permalink to this headline">¶</a></h1>
 <p>MDAnalysis reads coordinates from PDB files and additional optional
 data such as B-factors. It is also possible to substitute a PDB file
 instead of PSF file in order to define the list of atoms (but no
@@ -123,14 +123,14 @@ <h1>5.11. PDB structure files in MDAnalysis &#8212; <a class="reference internal
 recognized; the only difference is thath the single-frame PDB is represented as
 a trajectory with only one frame.</p>
 <p>In order to write a selection to a PDB file one typically uses the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.write" title="MDAnalysis.core.AtomGroup.AtomGroup.write"><tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.write()</span></tt></a> method of the selection:</p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.write" title="MDAnalysis.core.AtomGroup.AtomGroup.write"><code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.write()</span></code></a> method of the selection:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">calphas</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;name CA&quot;</span><span class="p">)</span>
 <span class="n">calphas</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&quot;calpha_only.pdb&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
 <p>This uses the coordinates from the current timestep of the trajectory.</p>
 <p>In order to write a PDB trajectory one needs to first obtain a multi-frame
-writer (keyword <em>multiframe</em> = <tt class="docutils literal"><span class="pre">True</span></tt>) and then iterate through the
+writer (keyword <em>multiframe</em> = <code class="docutils literal"><span class="pre">True</span></code>) and then iterate through the
 trajectory, while writing each frame:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">calphas</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;name CA&quot;</span><span class="p">)</span>
 <span class="n">W</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">Writer</span><span class="p">(</span><span class="s">&quot;calpha_traj.pdb&quot;</span><span class="p">,</span> <span class="n">multiframe</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
@@ -144,43 +144,43 @@ <h1>5.11. PDB structure files in MDAnalysis &#8212; <a class="reference internal
 standard</a>.</p>
 <div class="section" id="implementations">
 <h2>5.11.1. Implementations<a class="headerlink" href="#implementations" title="Permalink to this headline">¶</a></h2>
-<p>Two different implementations of PDB I/O are available: the &#8220;<a class="reference internal" href="#permissive"><em>permissive</em></a>&#8221;
-and the &#8220;<a class="reference internal" href="#strict"><em>strict</em></a>&#8221; Reader/Writers. The default are the &#8220;permissive&#8221; ones
+<p>Two different implementations of PDB I/O are available: the &#8220;<a class="reference internal" href="#permissive"><span>permissive</span></a>&#8221;
+and the &#8220;<a class="reference internal" href="#strict"><span>strict</span></a>&#8221; Reader/Writers. The default are the &#8220;permissive&#8221; ones
 but this can be changed by setting the flag &#8220;permissive_pdb_reader&#8221; in
-<tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> (see <a class="reference internal" href="../core/init.html#flags-label"><em>Flags</em></a>) to <tt class="docutils literal"><span class="pre">False</span></tt>:</p>
+<code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> (see <a class="reference internal" href="../core/init.html#flags-label"><span>Flags</span></a>) to <code class="docutils literal"><span class="pre">False</span></code>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&quot;permissive_pdb_reader&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">False</span>
 </pre></div>
 </div>
 <p>The <em>default for MDAnalysis</em> is to use the
-&#8220;<a class="reference internal" href="#permissive"><em>permissive</em></a>&#8221; <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></tt></a> and
-<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></tt></a>, corresponding to</p>
+&#8220;<a class="reference internal" href="#permissive"><span>permissive</span></a>&#8221; <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></code></a> and
+<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></code></a>, corresponding to</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&quot;permissive_pdb_reader&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span>
 </pre></div>
 </div>
 <p>On a case-by-case basis one kind of reader can be selected with the
-<em>permissive</em> keyword to <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>, e.g.</p>
+<em>permissive</em> keyword to <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>, e.g.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">u</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="n">PDB</span><span class="p">,</span> <span class="n">permissive</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>would select <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBReader" title="MDAnalysis.coordinates.PDB.PDBReader"><tt class="xref py py-class docutils literal"><span class="pre">PDBReader</span></tt></a> instead of the default
-<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></tt></a>.</p>
+<p>would select <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBReader" title="MDAnalysis.coordinates.PDB.PDBReader"><code class="xref py py-class docutils literal"><span class="pre">PDBReader</span></code></a> instead of the default
+<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></code></a>.</p>
 </div>
 <div class="section" id="simple-permissive-pdb-reader-and-writer">
 <span id="permissive"></span><h2>5.11.2. Simple (permissive) PDB Reader and Writer<a class="headerlink" href="#simple-permissive-pdb-reader-and-writer" title="Permalink to this headline">¶</a></h2>
 <p>A pure-Python implementation for PDB files commonly encountered in MD
-simulations comes under the names <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></tt></a> and
-<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></tt></a>. It only implements a subset of the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/v3.2.html">PDB standard</a>
+simulations comes under the names <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></code></a> and
+<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></code></a>. It only implements a subset of the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/v3.2.html">PDB standard</a>
 (for instance, it does not deal with insertion codes) and also allows some
 typical enhancements such as 4-letter resids (introduced by CHARMM/NAMD). The
 &#8220;primitive PDB Reader/Writer&#8221; are the <em>default</em> in MDAnalysis (equivalent to
-supplying the <em>permissive</em> = <tt class="docutils literal"><span class="pre">True</span></tt> keyword to
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>).</p>
-<p>The <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></tt></a> can read multi-frame PDB files and represents
-them as a trajectory. The <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></tt></a> can write single and
+supplying the <em>permissive</em> = <code class="docutils literal"><span class="pre">True</span></code> keyword to
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>).</p>
+<p>The <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></code></a> can read multi-frame PDB files and represents
+them as a trajectory. The <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></code></a> can write single and
 multi-frame PDB files as specified by the <em>multiframe</em> keyword. By default, it
-writes single frames. On the other hand, the <a class="reference internal" href="#MDAnalysis.coordinates.PDB.MultiPDBWriter" title="MDAnalysis.coordinates.PDB.MultiPDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">MultiPDBWriter</span></tt></a> is set up
+writes single frames. On the other hand, the <a class="reference internal" href="#MDAnalysis.coordinates.PDB.MultiPDBWriter" title="MDAnalysis.coordinates.PDB.MultiPDBWriter"><code class="xref py py-class docutils literal"><span class="pre">MultiPDBWriter</span></code></a> is set up
 to write a PDB trajectory by default (equivalent to using <em>multiframe</em> =
-<tt class="docutils literal"><span class="pre">True</span></tt>).</p>
+<code class="docutils literal"><span class="pre">True</span></code>).</p>
 <div class="section" id="examples">
 <h3>5.11.2.1. Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
 <p>In order to write a <strong>multi-frame PDB trajectory</strong> from a universe <em>u</em> one can
@@ -200,14 +200,14 @@ <h3>5.11.2.1. Examples<a class="headerlink" href="#examples" title="Permalink to
 </pre></div>
 </div>
 <p>A single frame can be written with the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.write" title="MDAnalysis.core.AtomGroup.AtomGroup.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a> method of any
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>:</p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.write" title="MDAnalysis.core.AtomGroup.AtomGroup.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a> method of any
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">protein</span> <span class="o">=</span> <span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;protein&quot;</span><span class="p">)</span>
 <span class="n">protein</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&quot;protein.pdb&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
 <p>Alternatively, get the single frame writer and supply the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>:</p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">pdb</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">Writer</span><span class="p">(</span><span class="s">&quot;protein.pdb&quot;</span><span class="p">)</span>
 <span class="n">protein</span> <span class="o">=</span> <span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;protein&quot;</span><span class="p">)</span>
 <span class="n">pdb</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">protein</span><span class="p">)</span>
@@ -219,15 +219,15 @@ <h3>5.11.2.1. Examples<a class="headerlink" href="#examples" title="Permalink to
 <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h3>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PDB.</tt><tt class="descname">PrimitivePDBReader</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.PDB.</code><code class="descname">PrimitivePDBReader</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>PDBReader that reads a <a class="reference external" href="http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html">PDB-formatted</a> file, no frills.</p>
 <p>The following <em>PDB records</em> are parsed (see <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html">PDB coordinate section</a> for details):</p>
 <blockquote>
 <div><ul class="simple">
 <li><em>CRYST1</em> for unitcell A,B,C, alpha,beta,gamma</li>
 <li><em>ATOM</em> or <em>HETATM</em> for serial,name,resName,chainID,resSeq,x,y,z,occupancy,tempFactor</li>
-<li><em>HEADER</em> (<tt class="xref py py-attr docutils literal"><span class="pre">header</span></tt>), <em>TITLE</em> (<tt class="xref py py-attr docutils literal"><span class="pre">title</span></tt>), <em>COMPND</em>
-(<tt class="xref py py-attr docutils literal"><span class="pre">compound</span></tt>), <em>REMARK</em> (<tt class="xref py py-attr docutils literal"><span class="pre">remarks</span></tt>)</li>
+<li><em>HEADER</em> (<code class="xref py py-attr docutils literal"><span class="pre">header</span></code>), <em>TITLE</em> (<code class="xref py py-attr docutils literal"><span class="pre">title</span></code>), <em>COMPND</em>
+(<code class="xref py py-attr docutils literal"><span class="pre">compound</span></code>), <em>REMARK</em> (<code class="xref py py-attr docutils literal"><span class="pre">remarks</span></code>)</li>
 <li>all other lines are ignored</li>
 </ul>
 </div></blockquote>
@@ -364,15 +364,16 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></tt></a>; <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBReader" title="MDAnalysis.coordinates.PDB.PDBReader"><tt class="xref py py-class docutils literal"><span class="pre">PDBReader</span></tt></a>
+<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></code></a>; <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBReader" title="MDAnalysis.coordinates.PDB.PDBReader"><code class="xref py py-class docutils literal"><span class="pre">PDBReader</span></code></a>
 implements a larger subset of the header records,
-which are accessible as <tt class="xref py py-attr docutils literal"><span class="pre">PDBReader.metadata</span></tt>.</p>
+which are accessible as <code class="xref py py-attr docutils literal"><span class="pre">PDBReader.metadata</span></code>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>* Frames now 0-based instead of 1-based
+* New <code class="xref py py-attr docutils literal"><span class="pre">title</span></code> (list with all TITLE lines).</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>* Frames now 0-based instead of 1-based
-* New <tt class="xref py py-attr docutils literal"><span class="pre">title</span></tt> (list with all TITLE lines).</p>
 <p>Read coordinates from <em>filename</em>.</p>
 <p><em>filename</em> can be a gzipped or bzip2ed compressed PDB file.</p>
 <p>If the pdb file contains multiple MODEL records then it is
@@ -381,20 +382,20 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 of integers (typically starting at 1 or 0).</p>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a permissive (simple) PDBWriter for <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output PDB file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></tt></a></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -403,7 +404,7 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBReader.get_occupancy">
-<tt class="descname">get_occupancy</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBReader.get_occupancy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader.get_occupancy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">get_occupancy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBReader.get_occupancy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader.get_occupancy" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return an array of occupancies in atom order.</p>
 </dd></dl>
 
@@ -411,35 +412,38 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PDB.</tt><tt class="descname">PrimitivePDBWriter</tt><big>(</big><em>filename</em>, <em>bonds='conect'</em>, <em>n_atoms=None</em>, <em>start=0</em>, <em>step=1</em>, <em>remarks='Created by PrimitivePDBWriter'</em>, <em>convert_units=None</em>, <em>multiframe=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.PDB.</code><code class="descname">PrimitivePDBWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>bonds='conect'</em>, <em>n_atoms=None</em>, <em>start=0</em>, <em>step=1</em>, <em>remarks='Created by PrimitivePDBWriter'</em>, <em>convert_units=None</em>, <em>multiframe=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>PDB writer that implements a subset of the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/v3.2.html">PDB 3.2 standard</a> .</p>
 <p>PDB format as used by NAMD/CHARMM: 4-letter resnames and segID are allowed,
 altLoc is written.</p>
-<p>The <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></tt></a> can be used to either a dump a coordinate
+<p>The <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></code></a> can be used to either a dump a coordinate
 set to a PDB file (operating as a &#8220;single frame writer&#8221;, selected with the
-constructor keyword <em>multiframe</em> = <tt class="docutils literal"><span class="pre">False</span></tt>, the default) or by writing a
-PDB &#8220;movie&#8221; (multi frame mode, <em>multiframe</em> = <tt class="docutils literal"><span class="pre">True</span></tt>), consisting of
+constructor keyword <em>multiframe</em> = <code class="docutils literal"><span class="pre">False</span></code>, the default) or by writing a
+PDB &#8220;movie&#8221; (multi frame mode, <em>multiframe</em> = <code class="docutils literal"><span class="pre">True</span></code>), consisting of
 multiple models (using the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#MODEL">MODEL</a> and <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#ENDMDL">ENDMDL</a> records).</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last">This class is identical to <a class="reference internal" href="#MDAnalysis.coordinates.PDB.MultiPDBWriter" title="MDAnalysis.coordinates.PDB.MultiPDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">MultiPDBWriter</span></tt></a> with the one
+<p class="last">This class is identical to <a class="reference internal" href="#MDAnalysis.coordinates.PDB.MultiPDBWriter" title="MDAnalysis.coordinates.PDB.MultiPDBWriter"><code class="xref py py-class docutils literal"><span class="pre">MultiPDBWriter</span></code></a> with the one
 exception that it defaults to writing single-frame PDB files as if
-<em>multiframe</em> = <tt class="docutils literal"><span class="pre">False</span></tt> was selected.</p>
+<em>multiframe</em> = <code class="docutils literal"><span class="pre">False</span></code> was selected.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Initial support for multi-frame PDB files.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>The <em>multiframe</em> keyword was added to select the writing mode. The writing
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Initial support for multi-frame PDB files.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>The <em>multiframe</em> keyword was added to select the writing mode. The writing
 of bond information (<a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect10.html#CONECT">CONECT</a> records) is now disabled by default but can be
 enabled with the <em>bonds</em> keyword.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 <p>Create a new PDBWriter</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of output file</p>
 </dd>
@@ -452,29 +456,29 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <dt><em>remarks</em></dt>
 <dd><p class="first last">comments to annotate pdb file (added to the TITLE record); note that
 any remarks from the trajectory that serves as input are
-written to REMARK records with lines longer than <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.remark_max_length" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.remark_max_length"><tt class="xref py py-attr docutils literal"><span class="pre">remark_max_length</span></tt></a> (66
+written to REMARK records with lines longer than <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.remark_max_length" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.remark_max_length"><code class="xref py py-attr docutils literal"><span class="pre">remark_max_length</span></code></a> (66
 characters) being wrapped.</p>
 </dd>
 <dt><em>convert_units</em></dt>
-<dd><p class="first last">units are converted to the MDAnalysis base format; <tt class="docutils literal"><span class="pre">None</span></tt> selects
-the value of <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> [&#8216;convert_lengths&#8217;]</p>
+<dd><p class="first last">units are converted to the MDAnalysis base format; <code class="docutils literal"><span class="pre">None</span></code> selects
+the value of <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> [&#8216;convert_lengths&#8217;]</p>
 </dd>
 <dt><em>bonds</em></dt>
-<dd><p class="first">write bonds to the PDB file as <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect10.html#CONECT">CONECT</a> records [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first">write bonds to the PDB file as <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect10.html#CONECT">CONECT</a> records [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 <div class="last admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">Currently only works when writing a whole <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> and
+<p class="last">Currently only works when writing a whole <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> and
 if bond information is available in the topology. (For selections
-smaller than the whole <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt>, the atom numbering in
+smaller than the whole <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code>, the atom numbering in
 the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect10.html#CONECT">CONECT</a> records would not match the numbering of the atoms in
-the new PDB file and therefore a <tt class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></tt> is
+the new PDB file and therefore a <code class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></code> is
 raised.)</p>
 </div>
 </dd>
 <dt><em>multiframe</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">False</span></tt>: write a single frame to the file; <tt class="docutils literal"><span class="pre">True</span></tt>: create a
+<dd><p class="first last"><code class="docutils literal"><span class="pre">False</span></code>: write a single frame to the file; <code class="docutils literal"><span class="pre">True</span></code>: create a
 multi frame PDB file in which frames are written as <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#MODEL">MODEL</a> ... <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#ENDMDL">ENDMDL</a>
-records. If <tt class="docutils literal"><span class="pre">None</span></tt>, then the class default is chosen.    [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+records. If <code class="docutils literal"><span class="pre">None</span></code>, then the class default is chosen.    [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -483,17 +487,17 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </table>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter._check_pdb_coordinates">
-<tt class="descname">_check_pdb_coordinates</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter._check_pdb_coordinates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter._check_pdb_coordinates" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_check_pdb_coordinates</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter._check_pdb_coordinates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter._check_pdb_coordinates" title="Permalink to this definition">¶</a></dt>
 <dd><p>Check if the coordinate values fall within the range allowed for PDB files.</p>
 <p>Deletes the output file if this is the first frame or if frames have
 already been written (in multi-frame mode) adds a REMARK instead of the
 coordinates and closes the file.</p>
-<p>Raises <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> if the coordinates fail the check.</p>
+<p>Raises <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> if the coordinates fail the check.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter._write_pdb_bonds">
-<tt class="descname">_write_pdb_bonds</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter._write_pdb_bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter._write_pdb_bonds" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_write_pdb_bonds</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter._write_pdb_bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter._write_pdb_bonds" title="Permalink to this definition">¶</a></dt>
 <dd><p>Writes out all the bond records; works only for Universe objects.</p>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
@@ -501,54 +505,56 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 incorrect. Once a selection is made, the atom numbers have to be
 updated (currently they are unmodified) and bonds have to be
 selected for, only if all the atoms for a bond are still present.</p>
-<p class="last">Therefore, this method raises a <tt class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></tt> if CONECT
-records for anything smaller than the <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> are written.</p>
+<p class="last">Therefore, this method raises a <code class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></code> if CONECT
+records for anything smaller than the <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> are written.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>Only write CONECT records if <code class="xref py py-attr docutils literal"><span class="pre">PrimitivePDBWriter.bonds</span></code> <code class="docutils literal"><span class="pre">==</span> <span class="pre">True</span></code>.
+Raises <code class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></code> if it would produce wrong output.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>Only write CONECT records if <tt class="xref py py-attr docutils literal"><span class="pre">PrimitivePDBWriter.bonds</span></tt> <tt class="docutils literal"><span class="pre">==</span> <span class="pre">True</span></tt>.
-Raises <tt class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></tt> if it would produce wrong output.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter._update_frame">
-<tt class="descname">_update_frame</tt><big>(</big><em>obj</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter._update_frame"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter._update_frame" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_update_frame</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter._update_frame"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter._update_frame" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to initialize important attributes in writer from a AtomGroup or Universe <em>obj</em>.</p>
 <p>Attributes initialized/updated:</p>
 <ul class="simple">
-<li><tt class="xref py py-attr docutils literal"><span class="pre">PrimitivePDBWriter.obj</span></tt> (the entity that provides topology information <em>and</em>
-coordinates, either a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> or a whole
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>)</li>
-<li><tt class="xref py py-attr docutils literal"><span class="pre">PrimitivePDBWriter.trajectory</span></tt> (the underlying trajectory
-<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><tt class="xref py py-class docutils literal"><span class="pre">Reader</span></tt></a>)</li>
-<li><tt class="xref py py-attr docutils literal"><span class="pre">PrimitivePDBWriter.timestep</span></tt> (the underlying trajectory
-<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>)</li>
+<li><code class="xref py py-attr docutils literal"><span class="pre">PrimitivePDBWriter.obj</span></code> (the entity that provides topology information <em>and</em>
+coordinates, either a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> or a whole
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>)</li>
+<li><code class="xref py py-attr docutils literal"><span class="pre">PrimitivePDBWriter.trajectory</span></code> (the underlying trajectory
+<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><code class="xref py py-class docutils literal"><span class="pre">Reader</span></code></a>)</li>
+<li><code class="xref py py-attr docutils literal"><span class="pre">PrimitivePDBWriter.timestep</span></code> (the underlying trajectory
+<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>)</li>
 </ul>
-<p>Before calling <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write_next_timestep" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write_next_timestep"><tt class="xref py py-meth docutils literal"><span class="pre">write_next_timestep()</span></tt></a> this method <strong>must</strong> be
+<p>Before calling <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write_next_timestep" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write_next_timestep"><code class="xref py py-meth docutils literal"><span class="pre">write_next_timestep()</span></code></a> this method <strong>must</strong> be
 called at least once to enable extracting topology information from the
 current frame.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter._write_timestep">
-<tt class="descname">_write_timestep</tt><big>(</big><em>ts</em>, <em>multiframe=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter._write_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter._write_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_write_timestep</code><span class="sig-paren">(</span><em>ts</em>, <em>multiframe=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter._write_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter._write_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a new timestep <em>ts</em> to file</p>
 <p>Does unit conversion if necessary.</p>
-<p>By setting <em>multiframe</em> = <tt class="docutils literal"><span class="pre">True</span></tt>, <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#MODEL">MODEL</a> ... <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#ENDMDL">ENDMDL</a> records are
+<p>By setting <em>multiframe</em> = <code class="docutils literal"><span class="pre">True</span></code>, <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#MODEL">MODEL</a> ... <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#ENDMDL">ENDMDL</a> records are
 written to represent trajectory frames in a multi-model PDB file. (At
 the moment we do <em>not</em> write the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect2.html#NUMMDL">NUMMDL</a> record.)</p>
-<p>The <em>multiframe</em> = <tt class="docutils literal"><span class="pre">False</span></tt> keyword signals that the
-<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></tt></a> is in single frame mode and no <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#MODEL">MODEL</a>
+<p>The <em>multiframe</em> = <code class="docutils literal"><span class="pre">False</span></code> keyword signals that the
+<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></code></a> is in single frame mode and no <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#MODEL">MODEL</a>
 records are written.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>The <em>multiframe</em> keyword was added, which completely determines if
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>The <em>multiframe</em> keyword was added, which completely determines if
 MODEL records are written. (Previously, this was decided based on the
-underlying trajectory and only if <tt class="docutils literal"><span class="pre">len(traj)</span> <span class="pre">&gt;</span> <span class="pre">1</span></tt> would MODEL records
+underlying trajectory and only if <code class="docutils literal"><span class="pre">len(traj)</span> <span class="pre">&gt;</span> <span class="pre">1</span></code> would MODEL records
 have been written.)</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ATOM">
-<tt class="descname">ATOM</tt><big>(</big><em>serial=None</em>, <em>name=None</em>, <em>altLoc=None</em>, <em>resName=None</em>, <em>chainID=None</em>, <em>resSeq=None</em>, <em>iCode=None</em>, <em>x=None</em>, <em>y=None</em>, <em>z=None</em>, <em>occupancy=1.0</em>, <em>tempFactor=0.0</em>, <em>segID=None</em>, <em>element=None</em>, <em>charge=0</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.ATOM"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ATOM" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ATOM</code><span class="sig-paren">(</span><em>serial=None</em>, <em>name=None</em>, <em>altLoc=None</em>, <em>resName=None</em>, <em>chainID=None</em>, <em>resSeq=None</em>, <em>iCode=None</em>, <em>x=None</em>, <em>y=None</em>, <em>z=None</em>, <em>occupancy=1.0</em>, <em>tempFactor=0.0</em>, <em>segID=None</em>, <em>element=None</em>, <em>charge=0</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.ATOM"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ATOM" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html">ATOM</a> record.</p>
 <p>Only some keword args are optional (<em>altLoc</em>, <em>iCode</em>, <em>chainID</em>), for
 some defaults are set.</p>
@@ -559,54 +565,55 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 special value &#8220;SYSTEM&#8221; (assigned by MDAnalysis if neither <em>segID</em> nor
 <em>chainID</em> were available), in which case the PDB will have an empty
 <em>chainID</em>).</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>If the <em>chainID</em> has the special value &#8220;SYSTEM&#8221; (case insensitive)
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>If the <em>chainID</em> has the special value &#8220;SYSTEM&#8221; (case insensitive)
 then the chain is set to the empty string &#8220;&#8221;.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.CONECT">
-<tt class="descname">CONECT</tt><big>(</big><em>conect</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.CONECT"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.CONECT" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CONECT</code><span class="sig-paren">(</span><em>conect</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.CONECT"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.CONECT" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect10.html#CONECT">CONECT</a> record.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.CRYST1">
-<tt class="descname">CRYST1</tt><big>(</big><em>dimensions</em>, <em>spacegroup='P 1'</em>, <em>zvalue=1</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.CRYST1"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.CRYST1" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CRYST1</code><span class="sig-paren">(</span><em>dimensions</em>, <em>spacegroup='P 1'</em>, <em>zvalue=1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.CRYST1"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.CRYST1" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect8.html">CRYST1</a> record.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.END">
-<tt class="descname">END</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.END"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.END" title="Permalink to this definition">¶</a></dt>
+<code class="descname">END</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.END"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.END" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect11.html#END">END</a> record.</p>
 <p>Only a single END record is written. Calling END multiple times has no
-effect. Because <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.close" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.close"><tt class="xref py py-meth docutils literal"><span class="pre">close()</span></tt></a> also calls this
+effect. Because <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.close" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.close"><code class="xref py py-meth docutils literal"><span class="pre">close()</span></code></a> also calls this
 method right before closing the file it is recommended to <em>not</em> call
-<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.END" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.END"><tt class="xref py py-meth docutils literal"><span class="pre">END()</span></tt></a> explicitly.</p>
+<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.END" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.END"><code class="xref py py-meth docutils literal"><span class="pre">END()</span></code></a> explicitly.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ENDMDL">
-<tt class="descname">ENDMDL</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.ENDMDL"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ENDMDL" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ENDMDL</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.ENDMDL"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ENDMDL" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#ENDMDL">ENDMDL</a> record.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.HEADER">
-<tt class="descname">HEADER</tt><big>(</big><em>trajectory</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.HEADER"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.HEADER" title="Permalink to this definition">¶</a></dt>
+<code class="descname">HEADER</code><span class="sig-paren">(</span><em>trajectory</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.HEADER"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.HEADER" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect2.html#HEADER">HEADER</a> record.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.MODEL">
-<tt class="descname">MODEL</tt><big>(</big><em>modelnumber</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.MODEL"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.MODEL" title="Permalink to this definition">¶</a></dt>
+<code class="descname">MODEL</code><span class="sig-paren">(</span><em>modelnumber</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.MODEL"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.MODEL" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#MODEL">MODEL</a> record.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.REMARK">
-<tt class="descname">REMARK</tt><big>(</big><em>*remarks</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.REMARK"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.REMARK" title="Permalink to this definition">¶</a></dt>
+<code class="descname">REMARK</code><span class="sig-paren">(</span><em>*remarks</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.REMARK"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.REMARK" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write generic <a class="reference external" href="http://www.wwpdb.org/documentation/format32/remarks1.html">REMARK</a> record (without number).</p>
 <p>Each string provided in <em>remarks</em> is written as a separate <a class="reference external" href="http://www.wwpdb.org/documentation/format32/remarks1.html">REMARK</a>
 record.</p>
@@ -615,40 +622,40 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.TITLE">
-<tt class="descname">TITLE</tt><big>(</big><em>*title</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.TITLE"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.TITLE" title="Permalink to this definition">¶</a></dt>
+<code class="descname">TITLE</code><span class="sig-paren">(</span><em>*title</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.TITLE"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.TITLE" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect2.html">TITLE</a> record.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close PDB file and write END record</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.remark_max_length">
-<tt class="descname">remark_max_length</tt><em class="property"> = 66</em><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.remark_max_length" title="Permalink to this definition">¶</a></dt>
+<code class="descname">remark_max_length</code><em class="property"> = 66</em><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.remark_max_length" title="Permalink to this definition">¶</a></dt>
 <dd><p>wrap comments into REMARK records that are not longer than</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write">
-<tt class="descname">write</tt><big>(</big><em>obj</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write object <em>obj</em> at current trajectory frame to file.</p>
 <p><em>obj</em> can be a selection (i.e. a
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>) or a whole
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>.</p>
-<p>The last letter of the <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><tt class="xref py py-attr docutils literal"><span class="pre">segid</span></tt></a> is
-used as the PDB chainID (but see <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ATOM" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ATOM"><tt class="xref py py-meth docutils literal"><span class="pre">ATOM()</span></tt></a> for
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>) or a whole
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>.</p>
+<p>The last letter of the <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><code class="xref py py-attr docutils literal"><span class="pre">segid</span></code></a> is
+used as the PDB chainID (but see <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ATOM" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ATOM"><code class="xref py py-meth docutils literal"><span class="pre">ATOM()</span></code></a> for
 details).</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>obj</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> or
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a></p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> or
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a></p>
 </dd>
 </dl>
 </td>
@@ -659,10 +666,10 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write_all_timesteps">
-<tt class="descname">write_all_timesteps</tt><big>(</big><em>obj</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.write_all_timesteps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write_all_timesteps" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_all_timesteps</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.write_all_timesteps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write_all_timesteps" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write all timesteps associated with <em>obj</em> to the PDB file.</p>
-<p><em>obj</em> can be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
-or a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>.</p>
+<p><em>obj</em> can be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+or a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>.</p>
 <p>The method writes the frames from the one specified as <em>start</em> until
 the end, using a step of <em>skip</em> (<em>start</em> and <em>skip</em> are set in the
 constructor). Thus, if <em>u</em> is a Universe then</p>
@@ -677,25 +684,26 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </pre></div>
 </div>
 <p>will be writing frames 12, 14, 16, ...</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write_next_timestep">
-<tt class="descname">write_next_timestep</tt><big>(</big><em>ts=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.write_next_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_next_timestep</code><span class="sig-paren">(</span><em>ts=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PrimitivePDBWriter.write_next_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>write a new timestep to the PDB file</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>ts</em></dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">base.Timestep</span></tt> object containing coordinates to be written to trajectory file;
-if <tt class="docutils literal"><span class="pre">None</span></tt> then <tt class="xref py py-attr docutils literal"><span class="pre">PrimitivePDBWriter.ts`</span></tt> is tried.</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">base.Timestep</span></code> object containing coordinates to be written to trajectory file;
+if <code class="docutils literal"><span class="pre">None</span></code> then <code class="xref py py-attr docutils literal"><span class="pre">PrimitivePDBWriter.ts`</span></code> is tried.</p>
 </dd>
 <dt><em>multiframe</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">False</span></tt>: write a single frame (default); <tt class="docutils literal"><span class="pre">True</span></tt> behave as a trajectory writer</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">False</span></code>: write a single frame (default); <code class="docutils literal"><span class="pre">True</span></code> behave as a trajectory writer</p>
 </dd>
 </dl>
 </td>
@@ -704,9 +712,9 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">Before using this method with another <tt class="xref py py-class docutils literal"><span class="pre">base.Timestep</span></tt> in the <em>ts</em>
-argument, <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter._update_frame" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter._update_frame"><tt class="xref py py-meth docutils literal"><span class="pre">PrimitivePDBWriter._update_frame()</span></tt></a> <em>must</em> be called
-with the <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> as
+<p class="last">Before using this method with another <code class="xref py py-class docutils literal"><span class="pre">base.Timestep</span></code> in the <em>ts</em>
+argument, <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter._update_frame" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter._update_frame"><code class="xref py py-meth docutils literal"><span class="pre">PrimitivePDBWriter._update_frame()</span></code></a> <em>must</em> be called
+with the <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> as
 its argument so that topology information can be gathered.</p>
 </div>
 </dd></dl>
@@ -715,27 +723,28 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.PDB.MultiPDBWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PDB.</tt><tt class="descname">MultiPDBWriter</tt><big>(</big><em>filename</em>, <em>bonds='conect'</em>, <em>n_atoms=None</em>, <em>start=0</em>, <em>step=1</em>, <em>remarks='Created by PrimitivePDBWriter'</em>, <em>convert_units=None</em>, <em>multiframe=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#MultiPDBWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.MultiPDBWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.PDB.</code><code class="descname">MultiPDBWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>bonds='conect'</em>, <em>n_atoms=None</em>, <em>start=0</em>, <em>step=1</em>, <em>remarks='Created by PrimitivePDBWriter'</em>, <em>convert_units=None</em>, <em>multiframe=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#MultiPDBWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.MultiPDBWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>PDB writer that implements a subset of the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/v3.2.html">PDB 3.2 standard</a> .</p>
 <p>PDB format as used by NAMD/CHARMM: 4-letter resnames and segID, altLoc
 is written.</p>
-<p>By default, <a class="reference internal" href="#MDAnalysis.coordinates.PDB.MultiPDBWriter" title="MDAnalysis.coordinates.PDB.MultiPDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">MultiPDBWriter</span></tt></a> writes a PDB &#8220;movie&#8221; (multi frame mode,
-<em>multiframe</em> = <tt class="docutils literal"><span class="pre">True</span></tt>), consisting of multiple models (using the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#MODEL">MODEL</a>
+<p>By default, <a class="reference internal" href="#MDAnalysis.coordinates.PDB.MultiPDBWriter" title="MDAnalysis.coordinates.PDB.MultiPDBWriter"><code class="xref py py-class docutils literal"><span class="pre">MultiPDBWriter</span></code></a> writes a PDB &#8220;movie&#8221; (multi frame mode,
+<em>multiframe</em> = <code class="docutils literal"><span class="pre">True</span></code>), consisting of multiple models (using the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#MODEL">MODEL</a>
 and <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#ENDMDL">ENDMDL</a> records).</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last">This class is identical to <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></tt></a> with the one
+<p class="last">This class is identical to <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></code></a> with the one
 exception that it defaults to writing multi-frame PDB files instead of
 single frames.</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 <p>Create a new PDBWriter</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of output file</p>
 </dd>
@@ -748,29 +757,29 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <dt><em>remarks</em></dt>
 <dd><p class="first last">comments to annotate pdb file (added to the TITLE record); note that
 any remarks from the trajectory that serves as input are
-written to REMARK records with lines longer than <tt class="xref py py-attr docutils literal"><span class="pre">remark_max_length</span></tt> (66
+written to REMARK records with lines longer than <code class="xref py py-attr docutils literal"><span class="pre">remark_max_length</span></code> (66
 characters) being wrapped.</p>
 </dd>
 <dt><em>convert_units</em></dt>
-<dd><p class="first last">units are converted to the MDAnalysis base format; <tt class="docutils literal"><span class="pre">None</span></tt> selects
-the value of <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> [&#8216;convert_lengths&#8217;]</p>
+<dd><p class="first last">units are converted to the MDAnalysis base format; <code class="docutils literal"><span class="pre">None</span></code> selects
+the value of <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> [&#8216;convert_lengths&#8217;]</p>
 </dd>
 <dt><em>bonds</em></dt>
-<dd><p class="first">write bonds to the PDB file as <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect10.html#CONECT">CONECT</a> records [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first">write bonds to the PDB file as <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect10.html#CONECT">CONECT</a> records [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 <div class="last admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">Currently only works when writing a whole <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> and
+<p class="last">Currently only works when writing a whole <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> and
 if bond information is available in the topology. (For selections
-smaller than the whole <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt>, the atom numbering in
+smaller than the whole <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code>, the atom numbering in
 the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect10.html#CONECT">CONECT</a> records would not match the numbering of the atoms in
-the new PDB file and therefore a <tt class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></tt> is
+the new PDB file and therefore a <code class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></code> is
 raised.)</p>
 </div>
 </dd>
 <dt><em>multiframe</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">False</span></tt>: write a single frame to the file; <tt class="docutils literal"><span class="pre">True</span></tt>: create a
+<dd><p class="first last"><code class="docutils literal"><span class="pre">False</span></code>: write a single frame to the file; <code class="docutils literal"><span class="pre">True</span></code>: create a
 multi frame PDB file in which frames are written as <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#MODEL">MODEL</a> ... <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html#ENDMDL">ENDMDL</a>
-records. If <tt class="docutils literal"><span class="pre">None</span></tt>, then the class default is chosen.    [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+records. If <code class="docutils literal"><span class="pre">None</span></code>, then the class default is chosen.    [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -783,74 +792,75 @@ <h3>5.11.2.2. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </div>
 <div class="section" id="biopython-strict-pdb-reader-and-writer">
 <span id="strict"></span><h2>5.11.3. Biopython (strict) PDB Reader and Writer<a class="headerlink" href="#biopython-strict-pdb-reader-and-writer" title="Permalink to this headline">¶</a></h2>
-<p>The <tt class="xref py py-mod docutils literal"><span class="pre">PDB</span></tt> module can make use of Biopython&#8217;s <tt class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></tt>
-<a class="reference internal" href="#hamelryck2003">[Hamelryck2003]</a> but replaces the standard PDB file parser with one that uses
-the <a class="reference internal" href="pdbextensions.html#MDAnalysis.coordinates.pdb.extensions.SloppyStructureBuilder" title="MDAnalysis.coordinates.pdb.extensions.SloppyStructureBuilder"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.pdb.extensions.SloppyStructureBuilder</span></tt></a> to
+<p>The <code class="xref py py-mod docutils literal"><span class="pre">PDB</span></code> module can make use of Biopython&#8217;s <code class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></code>
+<a class="reference internal" href="#hamelryck2003" id="id17">[Hamelryck2003]</a> but replaces the standard PDB file parser with one that uses
+the <a class="reference internal" href="pdbextensions.html#MDAnalysis.coordinates.pdb.extensions.SloppyStructureBuilder" title="MDAnalysis.coordinates.pdb.extensions.SloppyStructureBuilder"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.pdb.extensions.SloppyStructureBuilder</span></code></a> to
 cope with very large pdb files as commonly encountered in MD simulations. The
-Biopython-based <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBReader" title="MDAnalysis.coordinates.PDB.PDBReader"><tt class="xref py py-class docutils literal"><span class="pre">PDBReader</span></tt></a> has the advantage that it implements the
+Biopython-based <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBReader" title="MDAnalysis.coordinates.PDB.PDBReader"><code class="xref py py-class docutils literal"><span class="pre">PDBReader</span></code></a> has the advantage that it implements the
 <a class="reference external" href="http://www.wwpdb.org/documentation/format32/v3.2.html">PDB standard</a> rigorously but this comes at the cost of flexibility and
 performance. It is also difficult to write out selections using this
-implementation (<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBWriter" title="MDAnalysis.coordinates.PDB.PDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PDBWriter</span></tt></a>) and multi frame PDB files are not
+implementation (<a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBWriter" title="MDAnalysis.coordinates.PDB.PDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PDBWriter</span></code></a>) and multi frame PDB files are not
 implemented. The Biopython Reader/Writer can be selected when loading data into
-a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> by providing the keyword
-<em>permissive</em> = <tt class="docutils literal"><span class="pre">False</span></tt>.</p>
-<p>The Biopython PDB parser <tt class="xref py py-class docutils literal"><span class="pre">Bio.PDB.PDBParser</span></tt> is fairly strict and even
+a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> by providing the keyword
+<em>permissive</em> = <code class="docutils literal"><span class="pre">False</span></code>.</p>
+<p>The Biopython PDB parser <code class="xref py py-class docutils literal"><span class="pre">Bio.PDB.PDBParser</span></code> is fairly strict and even
 in its own permissive mode (which MDAnalysis employs) typically warns about
 missing element names with a
-<tt class="xref py py-exc docutils literal"><span class="pre">Bio.PDB.PDBExceptions.PDBConstructionWarning</span></tt> . Such warnings, however,
+<code class="xref py py-exc docutils literal"><span class="pre">Bio.PDB.PDBExceptions.PDBConstructionWarning</span></code> . Such warnings, however,
 are generally harmless and therefore are filtered (and ignored) by MDAnalysis
-with the help of <a class="reference external" href="http://docs.python.org/library/warnings.html#warnings.filterwarnings" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">warnings.filterwarnings()</span></tt></a>.</p>
+with the help of <a class="reference external" href="http://docs.python.org/library/warnings.html#warnings.filterwarnings" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">warnings.filterwarnings()</span></code></a>.</p>
 <div class="section" id="id18">
 <h3>5.11.3.1. Classes<a class="headerlink" href="#id18" title="Permalink to this headline">¶</a></h3>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.PDB.PDBReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PDB.</tt><tt class="descname">PDBReader</tt><big>(</big><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PDBReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBReader" title="Permalink to this definition">¶</a></dt>
-<dd><p>Read a pdb file into a <tt class="xref py py-mod docutils literal"><span class="pre">BioPython.PDB</span></tt> structure.</p>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.PDB.</code><code class="descname">PDBReader</code><span class="sig-paren">(</span><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PDBReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBReader" title="Permalink to this definition">¶</a></dt>
+<dd><p>Read a pdb file into a <code class="xref py py-mod docutils literal"><span class="pre">BioPython.PDB</span></code> structure.</p>
 <p>The coordinates are also supplied as one numpy array and wrapped
 into a Timestep object.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The Biopython.PDB reader does not parse the <tt class="docutils literal"><span class="pre">CRYST1</span></tt>
+<p class="last">The Biopython.PDB reader does not parse the <code class="docutils literal"><span class="pre">CRYST1</span></code>
 record and hence the unitcell dimensions are not set.
-Use the <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></tt></a> instead (i.e.  use
-the <tt class="docutils literal"><span class="pre">primitive=True</span></tt> keyword for <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt>).</p>
+Use the <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></code></a> instead (i.e.  use
+the <code class="docutils literal"><span class="pre">primitive=True</span></code> keyword for <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code>).</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>* Frames now 0-based instead of 1-based. 
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>* Frames now 0-based instead of 1-based. 
 * All PDB header metadata parsed by the reader is available in
-  the dict <tt class="xref py py-attr docutils literal"><span class="pre">metadata</span></tt>.</p>
+  the dict <code class="xref py py-attr docutils literal"><span class="pre">metadata</span></code>.</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PDBReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PDBReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PDBReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a strict PDBWriter for <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output PDB file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBWriter" title="MDAnalysis.coordinates.PDB.PDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PDBWriter</span></tt></a></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBWriter" title="MDAnalysis.coordinates.PDB.PDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PDBWriter</span></code></a></p>
 </td>
 </tr>
 </tbody>
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">This <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBWriter" title="MDAnalysis.coordinates.PDB.PDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PDBWriter</span></tt></a> &#8216;s <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBWriter.write" title="MDAnalysis.coordinates.PDB.PDBWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a> method
-always requires a <tt class="xref py py-class docutils literal"><span class="pre">base.Timestep</span></tt> as an argument (it is
+<p class="last">This <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBWriter" title="MDAnalysis.coordinates.PDB.PDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PDBWriter</span></code></a> &#8216;s <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBWriter.write" title="MDAnalysis.coordinates.PDB.PDBWriter.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a> method
+always requires a <code class="xref py py-class docutils literal"><span class="pre">base.Timestep</span></code> as an argument (it is
 not optional anymore when the Writer is obtained through
-this method of <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBReader" title="MDAnalysis.coordinates.PDB.PDBReader"><tt class="xref py py-class docutils literal"><span class="pre">PDBReader</span></tt></a> .)</p>
+this method of <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBReader" title="MDAnalysis.coordinates.PDB.PDBReader"><code class="xref py py-class docutils literal"><span class="pre">PDBReader</span></code></a> .)</p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PDBReader.get_bfactors">
-<tt class="descname">get_bfactors</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PDBReader.get_bfactors"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBReader.get_bfactors" title="Permalink to this definition">¶</a></dt>
+<code class="descname">get_bfactors</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PDBReader.get_bfactors"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBReader.get_bfactors" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return an array of bfactors (tempFactor) in atom order.</p>
 </dd></dl>
 
@@ -858,28 +868,28 @@ <h3>5.11.3.1. Classes<a class="headerlink" href="#id18" title="Permalink to this
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.PDB.PDBWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PDB.</tt><tt class="descname">PDBWriter</tt><big>(</big><em>pdbfilename</em>, <em>universe=None</em>, <em>multi=False</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PDBWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.PDB.</code><code class="descname">PDBWriter</code><span class="sig-paren">(</span><em>pdbfilename</em>, <em>universe=None</em>, <em>multi=False</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PDBWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write out the current time step as a pdb file.</p>
 <p>This is not cleanly implemented at the moment. One must supply a
 universe, even though this is nominally an optional argument. The
 class behaves slightly differently depending on if the structure
-was loaded from a PDB (then the full-fledged <tt class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></tt> writer is
+was loaded from a PDB (then the full-fledged <code class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></code> writer is
 used) or if this is really only an atom selection (then a less
 sophistiocated writer is employed).</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The standard PDBWriter can only write the <em>whole system</em>.  In
-order to write a selection, use the <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></tt></a> ,
+order to write a selection, use the <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></code></a> ,
 which happens automatically when the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.write" title="MDAnalysis.core.AtomGroup.AtomGroup.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a> method of a
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> instance is used.</p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.write" title="MDAnalysis.core.AtomGroup.AtomGroup.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a> method of a
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> instance is used.</p>
 </div>
 <p>pdbwriter = PDBWriter(&lt;pdbfilename&gt;,universe=universe,**kwargs)</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt>pdbfilename     filename; if multi=True, embed a %%d formatstring</dt>
 <dd><p class="first last">so that write_next_timestep() can insert the frame number</p>
 </dd>
@@ -896,7 +906,7 @@ <h3>5.11.3.1. Classes<a class="headerlink" href="#id18" title="Permalink to this
 </table>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDB.PDBWriter.write">
-<tt class="descname">write</tt><big>(</big><em>ts=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PDBWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>ts=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDB.html#PDBWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write timestep as a pdb file.</p>
 <p>If ts=None then we try to get the current one from the universe.</p>
 </dd></dl>
@@ -923,7 +933,7 @@ <h2>5.11.4. References<a class="headerlink" href="#references" title="Permalink
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -938,11 +948,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="MOL2.html" title="5.10. MOL2 file format — MDAnalysis.coordinates.MOL2"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -952,7 +962,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/PDBQT.html b/package/doc/html/documentation_pages/coordinates/PDBQT.html
index bad91c9d790..173fac32594 100644
--- a/package/doc/html/documentation_pages/coordinates/PDBQT.html
+++ b/package/doc/html/documentation_pages/coordinates/PDBQT.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
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   <span class="target" id="module-MDAnalysis.coordinates.PDBQT"></span><div class="section" id="pdbqt-structure-files-in-mdanalysis-mdanalysis-coordinates-pdbqt">
-<h1>5.12. PDBQT structure files in MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.PDBQT" title="MDAnalysis.coordinates.PDBQT"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDBQT</span></tt></a><a class="headerlink" href="#pdbqt-structure-files-in-mdanalysis-mdanalysis-coordinates-pdbqt" title="Permalink to this headline">¶</a></h1>
+<h1>5.12. PDBQT structure files in MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.PDBQT" title="MDAnalysis.coordinates.PDBQT"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDBQT</span></code></a><a class="headerlink" href="#pdbqt-structure-files-in-mdanalysis-mdanalysis-coordinates-pdbqt" title="Permalink to this headline">¶</a></h1>
 <p>MDAnalysis reads coordinates from <a class="reference external" href="http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file">PDBQT</a> files and additional optional
 data such as B-factors, partial charge and <a class="reference external" href="http://autodock.scripps.edu/">AutoDock</a> atom types.  It
 is also possible to substitute a PDBQT file for a PSF file in order to
@@ -101,7 +101,7 @@ <h1>5.12. PDBQT structure files in MDAnalysis &#8212; <a class="reference intern
 available in this case).</p>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.PDBQT.PDBQTReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PDBQT.</tt><tt class="descname">PDBQTReader</tt><big>(</big><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.PDBQT.</code><code class="descname">PDBQTReader</code><span class="sig-paren">(</span><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>PDBQTReader that reads a PDBQT-formatted file, no frills.</p>
 <dl class="docutils">
 <dt>Records read:</dt>
@@ -240,9 +240,9 @@ <h1>5.12. PDBQT structure files in MDAnalysis &#8212; <a class="reference intern
 </tbody>
 </table>
 <p>We ignore torsion notation and just pull the partial charge and atom type columns:</p>
-<div class="highlight-python"><pre>COMPND    NSC7810
+<div class="highlight-python"><div class="highlight"><pre>COMPND    NSC7810
 REMARK  3 active torsions:
-REMARK  status: ('A' for Active; 'I' for Inactive)
+REMARK  status: (&#39;A&#39; for Active; &#39;I&#39; for Inactive)
 REMARK    1  A    between atoms: A7_7  and  C22_23
 REMARK    2  A    between atoms: A9_9  and  A11_11
 REMARK    3  A    between atoms: A17_17  and  C21_21
@@ -282,26 +282,28 @@ <h1>5.12. PDBQT structure files in MDAnalysis &#8212; <a class="reference intern
 ATOM     26  O4  INH I          -4.659   1.196   1.059  0.00  0.00    -0.644 OA
 ENDBRANCH   7  24
 TORSDOF 3
-123456789.123456789.123456789.123456789.123456789.123456789.123456789.123456789. (column reference)</pre>
+123456789.123456789.123456789.123456789.123456789.123456789.123456789.123456789. (column reference)
+</pre></div>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDBQT.PDBQTReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a permissive (simple) PDBQTWriter for <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output PDBQT file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter" title="MDAnalysis.coordinates.PDBQT.PDBQTWriter"><tt class="xref py py-class docutils literal"><span class="pre">PDBQTWriter</span></tt></a></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter" title="MDAnalysis.coordinates.PDBQT.PDBQTWriter"><code class="xref py py-class docutils literal"><span class="pre">PDBQTWriter</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -310,13 +312,13 @@ <h1>5.12. PDBQT structure files in MDAnalysis &#8212; <a class="reference intern
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDBQT.PDBQTReader.get_bfactors">
-<tt class="descname">get_bfactors</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTReader.get_bfactors"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTReader.get_bfactors" title="Permalink to this definition">¶</a></dt>
+<code class="descname">get_bfactors</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTReader.get_bfactors"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTReader.get_bfactors" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return an array of bfactors (tempFactor) in atom order.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDBQT.PDBQTReader.get_occupancy">
-<tt class="descname">get_occupancy</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTReader.get_occupancy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTReader.get_occupancy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">get_occupancy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTReader.get_occupancy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTReader.get_occupancy" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return an array of occupancies in atom order.</p>
 </dd></dl>
 
@@ -324,11 +326,11 @@ <h1>5.12. PDBQT structure files in MDAnalysis &#8212; <a class="reference intern
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.PDBQT.PDBQTWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PDBQT.</tt><tt class="descname">PDBQTWriter</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.PDBQT.</code><code class="descname">PDBQTWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>PDBQT writer that implements a subset of the <a class="reference external" href="http://www.wwpdb.org/documentation/format32/v3.2.html">PDB</a> 3.2 standard and the <a class="reference external" href="http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file">PDBQT</a> spec.</p>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDBQT.PDBQTWriter.ATOM">
-<tt class="descname">ATOM</tt><big>(</big><em>serial=None</em>, <em>name=None</em>, <em>altLoc=None</em>, <em>resName=None</em>, <em>chainID=None</em>, <em>resSeq=None</em>, <em>iCode=None</em>, <em>x=None</em>, <em>y=None</em>, <em>z=None</em>, <em>occupancy=1.0</em>, <em>tempFactor=0.0</em>, <em>segID=None</em>, <em>partialCharge=None</em>, <em>atomtype=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter.ATOM"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter.ATOM" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ATOM</code><span class="sig-paren">(</span><em>serial=None</em>, <em>name=None</em>, <em>altLoc=None</em>, <em>resName=None</em>, <em>chainID=None</em>, <em>resSeq=None</em>, <em>iCode=None</em>, <em>x=None</em>, <em>y=None</em>, <em>z=None</em>, <em>occupancy=1.0</em>, <em>tempFactor=0.0</em>, <em>segID=None</em>, <em>partialCharge=None</em>, <em>atomtype=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter.ATOM"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter.ATOM" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write ATOM record.
 <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html">http://www.wwpdb.org/documentation/format32/sect9.html</a>
 Only some keyword args are optional (altLoc, iCode, chainID), for some defaults are set.</p>
@@ -341,14 +343,14 @@ <h1>5.12. PDBQT structure files in MDAnalysis &#8212; <a class="reference intern
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDBQT.PDBQTWriter.CRYST1">
-<tt class="descname">CRYST1</tt><big>(</big><em>dimensions</em>, <em>spacegroup='P 1'</em>, <em>zvalue=1</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter.CRYST1"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter.CRYST1" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CRYST1</code><span class="sig-paren">(</span><em>dimensions</em>, <em>spacegroup='P 1'</em>, <em>zvalue=1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter.CRYST1"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter.CRYST1" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write CRYST1 record.
 <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect8.html">http://www.wwpdb.org/documentation/format32/sect8.html</a></p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDBQT.PDBQTWriter.REMARK">
-<tt class="descname">REMARK</tt><big>(</big><em>*remark</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter.REMARK"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter.REMARK" title="Permalink to this definition">¶</a></dt>
+<code class="descname">REMARK</code><span class="sig-paren">(</span><em>*remark</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter.REMARK"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter.REMARK" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write generic REMARK record (without number).
 <a class="reference external" href="http://www.wwpdb.org/documentation/format32/remarks1.html">http://www.wwpdb.org/documentation/format32/remarks1.html</a>
 <a class="reference external" href="http://www.wwpdb.org/documentation/format32/remarks2.html">http://www.wwpdb.org/documentation/format32/remarks2.html</a></p>
@@ -356,23 +358,23 @@ <h1>5.12. PDBQT structure files in MDAnalysis &#8212; <a class="reference intern
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDBQT.PDBQTWriter.TITLE">
-<tt class="descname">TITLE</tt><big>(</big><em>*title</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter.TITLE"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter.TITLE" title="Permalink to this definition">¶</a></dt>
+<code class="descname">TITLE</code><span class="sig-paren">(</span><em>*title</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter.TITLE"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter.TITLE" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write TITLE record.
 <a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect2.html">http://www.wwpdb.org/documentation/format32/sect2.html</a></p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PDBQT.PDBQTWriter.write">
-<tt class="descname">write</tt><big>(</big><em>selection</em>, <em>frame=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>selection</em>, <em>frame=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PDBQT.html#PDBQTWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PDBQT.PDBQTWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write selection at current trajectory frame to file.</p>
 <p>write(selection,frame=FRAME)</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>selection</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></p>
+<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a></p>
 </dd>
 <dt><em>frame</em></dt>
 <dd><p class="first last">optionally move to frame <em>FRAME</em></p>
@@ -385,11 +387,12 @@ <h1>5.12. PDBQT structure files in MDAnalysis &#8212; <a class="reference intern
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The first letter of the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><tt class="xref py py-attr docutils literal"><span class="pre">segid</span></tt></a> is used as the PDB
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><code class="xref py py-attr docutils literal"><span class="pre">segid</span></code></a> is used as the PDB
 chainID.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 </dd></dl>
 
 </dd></dl>
@@ -402,7 +405,7 @@ <h1>5.12. PDBQT structure files in MDAnalysis &#8212; <a class="reference intern
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
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-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -431,7 +434,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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 </html>
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diff --git a/package/doc/html/documentation_pages/coordinates/PQR.html b/package/doc/html/documentation_pages/coordinates/PQR.html
index d1fe6119f21..dcd3cf6e486 100644
--- a/package/doc/html/documentation_pages/coordinates/PQR.html
+++ b/package/doc/html/documentation_pages/coordinates/PQR.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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@@ -8,7 +6,7 @@
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-    <title>5.13. PQR file format — MDAnalysis.coordinates.PQR &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.13. PQR file format — MDAnalysis.coordinates.PQR &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
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@@ -16,7 +14,7 @@
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+        VERSION:     '0.11.0',
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         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
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-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.14. AMBER trajectories — MDAnalysis.coordinates.TRJ" href="TRJ.html" />
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+    <div class="related" role="navigation" aria-label="related navigation">
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-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/PQR.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.14. AMBER trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></code></a></p>
+  <div role="note" aria-label="source link">
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   <span class="target" id="module-MDAnalysis.coordinates.PQR"></span><div class="section" id="pqr-file-format-mdanalysis-coordinates-pqr">
-<h1>5.13. PQR file format &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.PQR" title="MDAnalysis.coordinates.PQR"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PQR</span></tt></a><a class="headerlink" href="#pqr-file-format-mdanalysis-coordinates-pqr" title="Permalink to this headline">¶</a></h1>
+<h1>5.13. PQR file format &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.PQR" title="MDAnalysis.coordinates.PQR"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PQR</span></code></a><a class="headerlink" href="#pqr-file-format-mdanalysis-coordinates-pqr" title="Permalink to this headline">¶</a></h1>
 <p>Read atoms with charges from a <a class="reference external" href="http://www.poissonboltzmann.org/file-formats/biomolecular-structurw/pqr">PQR</a> file (as written by <a class="reference external" href="http://www.poissonboltzmann.org/pdb2pqr">PDB2PQR</a>). The
 following is adopted from the description of the <a class="reference external" href="http://www.poissonboltzmann.org/file-formats/biomolecular-structurw/pqr">PQR</a> format as used by <a class="reference external" href="http://www.poissonboltzmann.org/apbs">APBS</a>:</p>
 <p><em>MDAnalysis</em> reads very loosely-formatted PQR files: all fields are
@@ -101,13 +101,15 @@ <h1>5.13. PQR file format &#8212; <a class="reference internal" href="#module-MD
 by the <a class="reference external" href="http://www.rcsb.org/pdb/info.html#File_Formats_and_Standards">PDB</a> format. This more liberal formatting allows coordinates
 which are larger/smaller than ±999 Å.</p>
 <p>MDAnalysis reads data on a per-line basis from PQR files using the following format:</p>
-<div class="highlight-python"><pre>recordName serial atomName residueName chainID residueNumber X Y Z charge radius</pre>
+<div class="highlight-python"><div class="highlight"><pre>recordName serial atomName residueName chainID residueNumber X Y Z charge radius
+</pre></div>
 </div>
 <p>If this fails it is assumed that the <em>chainID</em> was omitted and the shorter
 format is read:</p>
-<div class="highlight-python"><pre>recordName serial atomName residueName residueNumber X Y Z charge radius</pre>
+<div class="highlight-python"><div class="highlight"><pre>recordName serial atomName residueName residueNumber X Y Z charge radius
+</pre></div>
 </div>
-<p>Anything else will raise a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt>.</p>
+<p>Anything else will raise a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code>.</p>
 <p>The whitespace is the most important feature of this format: fields
 <em>must</em> be separated by at least one space or tab character. The fields
 are:</p>
@@ -145,36 +147,38 @@ <h1>5.13. PQR file format &#8212; <a class="reference internal" href="#module-MD
 </div>
 <p>For example, PQR files created with <a class="reference external" href="http://www.poissonboltzmann.org/pdb2pqr">PDB2PQR</a> and the <cite>&#8211;whitespace</cite>
 option are guaranteed to conform to the above format:</p>
-<div class="highlight-python"><pre>pdb2pqr --ff=charmm --whitespace 4ake.pdb 4ake.pqr</pre>
+<div class="highlight-python"><div class="highlight"><pre>pdb2pqr --ff=charmm --whitespace 4ake.pdb 4ake.pqr
+</pre></div>
 </div>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.PQR.PQRReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PQR.</tt><tt class="descname">PQRReader</tt><big>(</big><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.PQR.</code><code class="descname">PQRReader</code><span class="sig-paren">(</span><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read a <a class="reference external" href="http://www.poissonboltzmann.org/file-formats/biomolecular-structurw/pqr">PQR</a> file into MDAnalysis.</p>
-<p>The <a class="reference internal" href="../topology/PQRParser.html#module-MDAnalysis.topology.PQRParser" title="MDAnalysis.topology.PQRParser"><tt class="xref py py-mod docutils literal"><span class="pre">PQRParser</span></tt></a> takes charges from the
+<p>The <a class="reference internal" href="../topology/PQRParser.html#module-MDAnalysis.topology.PQRParser" title="MDAnalysis.topology.PQRParser"><code class="xref py py-mod docutils literal"><span class="pre">PQRParser</span></code></a> takes charges from the
 PQR file in order to populate the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.charge" title="MDAnalysis.core.AtomGroup.Atom.charge"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.charge</span></tt></a> attribute. Radii are
-accessible through the <a class="reference internal" href="#MDAnalysis.coordinates.PQR.PQRReader.get_radii" title="MDAnalysis.coordinates.PQR.PQRReader.get_radii"><tt class="xref py py-meth docutils literal"><span class="pre">get_radii()</span></tt></a> method of the reader, the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.radii" title="MDAnalysis.core.AtomGroup.AtomGroup.radii"><tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.radii()</span></tt></a> method and the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.radius" title="MDAnalysis.core.AtomGroup.Atom.radius"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.radius</span></tt></a> attribute.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.charge" title="MDAnalysis.core.AtomGroup.Atom.charge"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.charge</span></code></a> attribute. Radii are
+accessible through the <a class="reference internal" href="#MDAnalysis.coordinates.PQR.PQRReader.get_radii" title="MDAnalysis.coordinates.PQR.PQRReader.get_radii"><code class="xref py py-meth docutils literal"><span class="pre">get_radii()</span></code></a> method of the reader, the
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.radii" title="MDAnalysis.core.AtomGroup.AtomGroup.radii"><code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.radii()</span></code></a> method and the
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.radius" title="MDAnalysis.core.AtomGroup.Atom.radius"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.radius</span></code></a> attribute.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PQR.PQRReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a PQRWriter for <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output PQR file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.PQR.PQRWriter" title="MDAnalysis.coordinates.PQR.PQRWriter"><tt class="xref py py-class docutils literal"><span class="pre">PQRWriter</span></tt></a></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.PQR.PQRWriter" title="MDAnalysis.coordinates.PQR.PQRWriter"><code class="xref py py-class docutils literal"><span class="pre">PQRWriter</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -183,13 +187,13 @@ <h1>5.13. PQR file format &#8212; <a class="reference internal" href="#module-MD
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PQR.PQRReader.get_charges">
-<tt class="descname">get_charges</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRReader.get_charges"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRReader.get_charges" title="Permalink to this definition">¶</a></dt>
+<code class="descname">get_charges</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRReader.get_charges"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRReader.get_charges" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return an array of charges in atom order.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PQR.PQRReader.get_radii">
-<tt class="descname">get_radii</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRReader.get_radii"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRReader.get_radii" title="Permalink to this definition">¶</a></dt>
+<code class="descname">get_radii</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRReader.get_radii"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRReader.get_radii" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return an array of atom radii in atom order.</p>
 </dd></dl>
 
@@ -197,27 +201,28 @@ <h1>5.13. PQR file format &#8212; <a class="reference internal" href="#module-MD
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.PQR.PQRWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PQR.</tt><tt class="descname">PQRWriter</tt><big>(</big><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.PQR.</code><code class="descname">PQRWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a single coordinate frame in whitespace-separated PQR format.</p>
 <p>Charges (&#8220;Q&#8221;) are taken from the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.charge" title="MDAnalysis.core.AtomGroup.Atom.charge"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.charge</span></tt></a> attribute while
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.charge" title="MDAnalysis.core.AtomGroup.Atom.charge"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.charge</span></code></a> attribute while
 radii are obtaine from the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.radius" title="MDAnalysis.core.AtomGroup.Atom.radius"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.radius</span></tt></a> attribute.</p>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.radius" title="MDAnalysis.core.AtomGroup.Atom.radius"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.radius</span></code></a> attribute.</p>
 <ul class="simple">
 <li>If the segid is &#8216;SYSTEM&#8217; then it will be set to the empty
 string. Otherwise the first letter will be used as the chain ID.</li>
 <li>The serial number always starts at 1 and increments sequentially
 for the atoms.</li>
 </ul>
-<p>The output format is similar to <tt class="docutils literal"><span class="pre">pdb2pqr</span> <span class="pre">--whitespace</span></tt>.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
+<p>The output format is similar to <code class="docutils literal"><span class="pre">pdb2pqr</span> <span class="pre">--whitespace</span></code>.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
 <p>Set up a PQRWriter with full whitespace separation.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">output filename</p>
 </dd>
@@ -232,13 +237,13 @@ <h1>5.13. PQR file format &#8212; <a class="reference internal" href="#module-MD
 </table>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.PQR.PQRWriter.write">
-<tt class="descname">write</tt><big>(</big><em>selection</em>, <em>frame=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>selection</em>, <em>frame=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/PQR.html#PQRWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.PQR.PQRWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write selection at current trajectory frame to file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><blockquote class="first">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><blockquote class="first">
 <div><dl class="docutils">
 <dt><em>selection</em></dt>
 <dd><p class="first last">MDAnalysis AtomGroup (selection or Universe.atoms)
@@ -263,8 +268,9 @@ <h1>5.13. PQR file format &#8212; <a class="reference internal" href="#module-MD
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 </dd></dl>
 
 </dd></dl>
@@ -277,7 +283,7 @@ <h1>5.13. PQR file format &#8212; <a class="reference internal" href="#module-MD
       </div>
       <div class="clearer"></div>
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-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
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-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
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     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
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@@ -306,7 +312,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/TRJ.html b/package/doc/html/documentation_pages/coordinates/TRJ.html
index d27bcd51ccc..0e45fc658c3 100644
--- a/package/doc/html/documentation_pages/coordinates/TRJ.html
+++ b/package/doc/html/documentation_pages/coordinates/TRJ.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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@@ -8,7 +6,7 @@
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+    <title>5.14. AMBER trajectories — MDAnalysis.coordinates.TRJ &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
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@@ -27,16 +25,16 @@
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-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
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-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.15. Gromacs TRR file IO — MDAnalysis.coordinates.TRR" href="TRR.html" />
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              accesskey="P">previous</a> |</li>
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-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
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   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.14. AMBER trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.14. AMBER trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></code></a><ul>
 <li><a class="reference internal" href="#ascii-traj-trajectories">5.14.1. ASCII TRAJ trajectories</a></li>
 <li><a class="reference internal" href="#binary-netcdf-trajectories">5.14.2. Binary NetCDF trajectories</a></li>
 </ul>
@@ -71,16 +69,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
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   <p class="topless"><a href="PQR.html"
-                        title="previous chapter">5.13. PQR file format &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.PQR</span></tt></a></p>
+                        title="previous chapter">5.13. PQR file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.PQR</span></code></a></p>
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-  <h3>This Page</h3>
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+                        title="next chapter">5.15. Gromacs TRR file IO &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRR</span></code></a></p>
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   <span class="target" id="module-MDAnalysis.coordinates.TRJ"></span><div class="section" id="amber-trajectories-mdanalysis-coordinates-trj">
-<h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.TRJ" title="MDAnalysis.coordinates.TRJ"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></tt></a><a class="headerlink" href="#amber-trajectories-mdanalysis-coordinates-trj" title="Permalink to this headline">¶</a></h1>
-<p><a class="reference external" href="http://ambermd.org">AMBER</a> can write <a class="reference internal" href="#ascii-trajectories"><em>ASCII trajectories</em></a> (&#8220;traj&#8221;) and
-<a class="reference internal" href="#netcdf-trajectories"><em>binary trajectories</em></a> (&#8220;netcdf&#8221;). MDAnalysis supports
+<h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.TRJ" title="MDAnalysis.coordinates.TRJ"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></code></a><a class="headerlink" href="#amber-trajectories-mdanalysis-coordinates-trj" title="Permalink to this headline">¶</a></h1>
+<p><a class="reference external" href="http://ambermd.org">AMBER</a> can write <a class="reference internal" href="#ascii-trajectories"><span>ASCII trajectories</span></a> (&#8220;traj&#8221;) and
+<a class="reference internal" href="#netcdf-trajectories"><span>binary trajectories</span></a> (&#8220;netcdf&#8221;). MDAnalysis supports
 reading of both formats and writing for the binary trajectories.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
@@ -117,41 +117,42 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
 <li>lengths in Angstrom (Å)</li>
 <li>time in ps (but see below)</li>
 </ul>
-<p>AMBER trajectory coordinate frames are based on a <a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep" title="MDAnalysis.coordinates.TRJ.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>
+<p>AMBER trajectory coordinate frames are based on a <a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep" title="MDAnalysis.coordinates.TRJ.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>
 object.</p>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.TRJ.Timestep">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRJ.</tt><tt class="descname">Timestep</tt><big>(</big><em>n_atoms</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.Timestep" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRJ.</code><code class="descname">Timestep</code><span class="sig-paren">(</span><em>n_atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.Timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>AMBER trajectory Timestep.</p>
 <p>The Timestep can be initialized with <em>arg</em> being an integer
 (the number of atoms) and an optional keyword argument <em>velocities</em> to
 allocate space for both coordinates and velocities;</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Added ability to contain Forces</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Added ability to contain Forces</p>
+</div>
 <p>Create a Timestep, representing a frame of a trajectory</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">The total number of atoms this Timestep describes</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>positions</em></dt>
-<dd><p class="first last">Whether this Timestep has position information [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has position information [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 <dt><em>velocities</em></dt>
-<dd><p class="first last">Whether this Timestep has velocity information [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has velocity information [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>forces</em></dt>
-<dd><p class="first last">Whether this Timestep has force information [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has force information [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>dt</em></dt>
-<dd><p class="first last">The time difference between frames (ps).  If <tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt>
+<dd><p class="first last">The time difference between frames (ps).  If <code class="xref py py-attr docutils literal"><span class="pre">time</span></code>
 is set, then <cite>dt</cite> will be ignored.</p>
 </dd>
 <dt><em>time_offset</em></dt>
@@ -162,30 +163,31 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Added keywords for positions, velocities and forces
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Added keywords for positions, velocities and forces
 Can add and remove position/velocity/force information by using
 the has_* attribute</p>
+</div>
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRJ.Timestep._pos">
-<tt class="descname">_pos</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.Timestep._pos" title="Permalink to this definition">¶</a></dt>
-<dd><p>coordinates of the atoms as a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> of shape <cite>(n_atoms, 3)</cite></p>
+<code class="descname">_pos</code><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.Timestep._pos" title="Permalink to this definition">¶</a></dt>
+<dd><p>coordinates of the atoms as a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> of shape <cite>(n_atoms, 3)</cite></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRJ.Timestep._velocities">
-<tt class="descname">_velocities</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.Timestep._velocities" title="Permalink to this definition">¶</a></dt>
-<dd><p>velocities of the atoms as a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> of shape <cite>(n_atoms, 3)</cite>;
+<code class="descname">_velocities</code><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.Timestep._velocities" title="Permalink to this definition">¶</a></dt>
+<dd><p>velocities of the atoms as a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> of shape <cite>(n_atoms, 3)</cite>;
 only available if the trajectory contains velocities or if the
-<em>velocities</em> = <tt class="docutils literal"><span class="pre">True</span></tt> keyword has been supplied.</p>
+<em>velocities</em> = <code class="docutils literal"><span class="pre">True</span></code> keyword has been supplied.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRJ.Timestep._forces">
-<tt class="descname">_forces</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.Timestep._forces" title="Permalink to this definition">¶</a></dt>
-<dd><p>forces of the atoms as a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> of shape <cite>(n_atoms, 3)</cite>;
+<code class="descname">_forces</code><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.Timestep._forces" title="Permalink to this definition">¶</a></dt>
+<dd><p>forces of the atoms as a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> of shape <cite>(n_atoms, 3)</cite>;
 only available if the trajectory contains forces or if the
-<em>forces</em> = <tt class="docutils literal"><span class="pre">True</span></tt> keyword has been supplied.</p>
+<em>forces</em> = <code class="docutils literal"><span class="pre">True</span></code> keyword has been supplied.</p>
 </dd></dl>
 
 </dd></dl>
@@ -193,7 +195,7 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
 <div class="section" id="ascii-traj-trajectories">
 <span id="ascii-trajectories"></span><h2>5.14.1. ASCII TRAJ trajectories<a class="headerlink" href="#ascii-traj-trajectories" title="Permalink to this headline">¶</a></h2>
 <p>ASCII <a class="reference external" href="http://ambermd.org">AMBER</a> TRJ coordinate files (as defined in <a class="reference external" href="http://ambermd.org/formats.html#trajectory">AMBER TRJ format</a>)
-are handled by the <a class="reference internal" href="#MDAnalysis.coordinates.TRJ.TRJReader" title="MDAnalysis.coordinates.TRJ.TRJReader"><tt class="xref py py-class docutils literal"><span class="pre">TRJReader</span></tt></a>. It is also possible to directly
+are handled by the <a class="reference internal" href="#MDAnalysis.coordinates.TRJ.TRJReader" title="MDAnalysis.coordinates.TRJ.TRJReader"><code class="xref py py-class docutils literal"><span class="pre">TRJReader</span></code></a>. It is also possible to directly
 read <em>bzip2</em> or <em>gzip</em> compressed files.</p>
 <p>AMBER ASCII trajectories are recognised by the suffix &#8216;.trj&#8217; or
 &#8216;.mdcrd&#8217; (possibly with an additional &#8216;.gz&#8217; or &#8216;.bz2&#8217;).</p>
@@ -212,43 +214,44 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
 </ul>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.TRJ.TRJReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRJ.</tt><tt class="descname">TRJReader</tt><big>(</big><em>filename</em>, <em>n_atoms=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#TRJReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.TRJReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRJ.</code><code class="descname">TRJReader</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#TRJReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.TRJReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>AMBER trajectory reader.</p>
 <p>Reads the ASCII formatted <a class="reference external" href="http://ambermd.org/formats.html#trajectory">AMBER TRJ format</a>. Periodic box information
 is auto-detected.</p>
 <p>The number of atoms in a timestep <em>must</em> be provided in the <cite>n_atoms</cite>
 keyword because it is not stored in the trajectory header and cannot be
-reliably autodetected. The constructor raises a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> if
-<cite>n_atoms</cite> is left at its default value of <tt class="docutils literal"><span class="pre">None</span></tt>.</p>
+reliably autodetected. The constructor raises a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> if
+<cite>n_atoms</cite> is left at its default value of <code class="docutils literal"><span class="pre">None</span></code>.</p>
 <p>The length of a timestep is not stored in the trajectory itself but can
 be set by passing the <cite>dt</cite> keyword argument to the constructor; it
 is assumed to be in ps. The default value is 1 ps.</p>
 <p>Functionality is currently limited to simple iteration over the
 trajectory.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based
 kwarg &#8216;delta&#8217; renamed to &#8216;dt&#8217;, for uniformity with other Readers</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRJ.TRJReader.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#TRJReader.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.TRJReader.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#TRJReader.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.TRJReader.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close trj trajectory file if it was open.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRJ.TRJReader.n_frames">
-<tt class="descname">n_frames</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#TRJReader.n_frames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.TRJReader.n_frames" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_frames</code><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.TRJReader.n_frames" title="Permalink to this definition">¶</a></dt>
 <dd><p>Number of frames (obtained from reading the whole trajectory).</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRJ.TRJReader.open_trajectory">
-<tt class="descname">open_trajectory</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#TRJReader.open_trajectory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.TRJReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
+<code class="descname">open_trajectory</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#TRJReader.open_trajectory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.TRJReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
 <dd><p>Open the trajectory for reading and load first frame.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRJ.TRJReader.rewind">
-<tt class="descname">rewind</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#TRJReader.rewind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.TRJReader.rewind" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rewind</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#TRJReader.rewind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.TRJReader.rewind" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reposition at the beginning of the trajectory</p>
 </dd></dl>
 
@@ -259,15 +262,15 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
 <span id="netcdf-trajectories"></span><h2>5.14.2. Binary NetCDF trajectories<a class="headerlink" href="#binary-netcdf-trajectories" title="Permalink to this headline">¶</a></h2>
 <p>The <a class="reference external" href="http://ambermd.org/netcdf/nctraj.html">AMBER netcdf</a> format make use of <a class="reference external" href="http://www.unidata.ucar.edu/software/netcdf">NetCDF</a> (Network Common Data
 Form) format. Such binary trajectories are recognized in MDAnalysis by
-the &#8216;.ncdf&#8217; suffix and read by the <a class="reference internal" href="#MDAnalysis.coordinates.TRJ.NCDFReader" title="MDAnalysis.coordinates.TRJ.NCDFReader"><tt class="xref py py-class docutils literal"><span class="pre">NCDFReader</span></tt></a>.</p>
+the &#8216;.ncdf&#8217; suffix and read by the <a class="reference internal" href="#MDAnalysis.coordinates.TRJ.NCDFReader" title="MDAnalysis.coordinates.TRJ.NCDFReader"><code class="xref py py-class docutils literal"><span class="pre">NCDFReader</span></code></a>.</p>
 <p>Binary trajectories can also contain velocities and forces, and can record the
 exact time
 step. In principle, the trajectories can be in different units than the AMBER
 defaults of ångström and picoseconds but at the moment MDAnalysis only supports
-those and will raise a <tt class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></tt> if anything else is detected.</p>
+those and will raise a <code class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></code> if anything else is detected.</p>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.TRJ.NCDFReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRJ.</tt><tt class="descname">NCDFReader</tt><big>(</big><em>filename</em>, <em>n_atoms=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRJ.</code><code class="descname">NCDFReader</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reader for <a class="reference external" href="http://ambermd.org/netcdf/nctraj.html">AMBER NETCDF format</a> (version 1.0).</p>
 <p>AMBER binary trajectories are automatically recognised by the
 file extension &#8221;.ncdf&#8221;.</p>
@@ -276,44 +279,46 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
 frames and therefore supports direct indexing (with 0-based frame
 indices) and full-feature trajectory iteration, including slicing.</p>
 <p>Velocities are autodetected and read into the
-<a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep._velocities" title="MDAnalysis.coordinates.TRJ.Timestep._velocities"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep._velocities</span></tt></a> attribute.</p>
+<a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep._velocities" title="MDAnalysis.coordinates.TRJ.Timestep._velocities"><code class="xref py py-attr docutils literal"><span class="pre">Timestep._velocities</span></code></a> attribute.</p>
 <p>Forces are autodetected and read into the
-<a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep._forces" title="MDAnalysis.coordinates.TRJ.Timestep._forces"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep._forces</span></tt></a> attribute.</p>
+<a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep._forces" title="MDAnalysis.coordinates.TRJ.Timestep._forces"><code class="xref py py-attr docutils literal"><span class="pre">Timestep._forces</span></code></a> attribute.</p>
 <p>Periodic unit cell information is detected and used to populate the
-<tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></tt> attribute. (If no unit cell is available in
-the trajectory, then <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></tt> will return
-<tt class="docutils literal"><span class="pre">[0,0,0,0,0,0]</span></tt>.)</p>
+<code class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></code> attribute. (If no unit cell is available in
+the trajectory, then <code class="xref py py-attr docutils literal"><span class="pre">Timestep.dimensions</span></code> will return
+<code class="docutils literal"><span class="pre">[0,0,0,0,0,0]</span></code>.)</p>
 <p>Current limitations:</p>
 <ul class="simple">
 <li>only trajectories with time in ps and lengths in Angstroem are processed</li>
 <li>scale_factors are not supported (and not checked)</li>
 </ul>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.TRJ.NCDFWriter" title="MDAnalysis.coordinates.TRJ.NCDFWriter"><tt class="xref py py-class docutils literal"><span class="pre">NCDFWriter</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.TRJ.NCDFWriter" title="MDAnalysis.coordinates.TRJ.NCDFWriter"><code class="xref py py-class docutils literal"><span class="pre">NCDFWriter</span></code></a></p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Added ability to read Forces</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frame labels now 0-based instead of 1-based
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Added ability to read Forces</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frame labels now 0-based instead of 1-based
 kwarg &#8216;delta&#8217; renamed to &#8216;dt&#8217;, for uniformity with other Readers</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRJ.NCDFReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a NCDFWriter for <em>filename</em> with the same parameters as this NCDF.</p>
 <p>All values can be changed through keyword arguments.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output NCDF trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">number of atoms</p>
 </dd>
@@ -326,7 +331,7 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.TRJ.NCDFWriter" title="MDAnalysis.coordinates.TRJ.NCDFWriter"><tt class="xref py py-class docutils literal"><span class="pre">NCDFWriter</span></tt></a></p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.TRJ.NCDFWriter" title="MDAnalysis.coordinates.TRJ.NCDFWriter"><code class="xref py py-class docutils literal"><span class="pre">NCDFWriter</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -335,37 +340,39 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRJ.NCDFReader.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFReader.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFReader.close" title="Permalink to this definition">¶</a></dt>
-<dd><p>Close trajectory; any further access will raise an <tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt></p>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFReader.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFReader.close" title="Permalink to this definition">¶</a></dt>
+<dd><p>Close trajectory; any further access will raise an <code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code></p>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.TRJ.NCDFWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRJ.</tt><tt class="descname">NCDFWriter</tt><big>(</big><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=1.0</em>, <em>remarks=None</em>, <em>convert_units=None</em>, <em>zlib=False</em>, <em>cmplevel=1</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRJ.</code><code class="descname">NCDFWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=1.0</em>, <em>remarks=None</em>, <em>convert_units=None</em>, <em>zlib=False</em>, <em>cmplevel=1</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Writer for <a class="reference external" href="http://ambermd.org/netcdf/nctraj.html">AMBER NETCDF format</a> (version 1.0).</p>
 <p>AMBER binary trajectories are automatically recognised by the
 file extension &#8221;.ncdf&#8221;.</p>
 <p>Velocities are written out if they are detected in the input
-<a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep" title="MDAnalysis.coordinates.TRJ.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>. The trajectories are always written with ångström
+<a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep" title="MDAnalysis.coordinates.TRJ.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>. The trajectories are always written with ångström
 for the lengths and picoseconds for the time (and hence Å/ps for
 velocities).</p>
 <p>Unit cell information is written if available.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.TRJ.NCDFReader" title="MDAnalysis.coordinates.TRJ.NCDFReader"><tt class="xref py py-class docutils literal"><span class="pre">NCDFReader</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.TRJ.NCDFReader" title="MDAnalysis.coordinates.TRJ.NCDFReader"><code class="xref py py-class docutils literal"><span class="pre">NCDFReader</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Added ability to write velocities and forces</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>kwarg &#8216;delta&#8217; renamed to &#8216;dt&#8217;, for uniformity with other Readers</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Added ability to write velocities and forces</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>kwarg &#8216;delta&#8217; renamed to &#8216;dt&#8217;, for uniformity with other Readers</p>
 <p>Create a new NCDFWriter</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of output file</p>
 </dd>
@@ -375,7 +382,7 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>start</em></dt>
 <dd><p class="first last">starting timestep</p>
 </dd>
@@ -386,21 +393,21 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
 <dd><p class="first last">timestep</p>
 </dd>
 <dt><em>convert_units</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: units are converted to the AMBER base format; <tt class="docutils literal"><span class="pre">None</span></tt> selects
-the value of <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> [&#8216;convert_lengths&#8217;].
-(see <a class="reference internal" href="../core/init.html#flags-label"><em>Flags</em></a>)</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: units are converted to the AMBER base format; <code class="docutils literal"><span class="pre">None</span></code> selects
+the value of <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> [&#8216;convert_lengths&#8217;].
+(see <a class="reference internal" href="../core/init.html#flags-label"><span>Flags</span></a>)</p>
 </dd>
 <dt><em>zlib</em></dt>
-<dd><p class="first last">compress data [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">compress data [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>cmplevel</em></dt>
 <dd><p class="first last">compression level (1-9) [1]</p>
 </dd>
 <dt><em>velocities</em></dt>
-<dd><p class="first last">Write velocities into the trajectory [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Write velocities into the trajectory [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>forces</em></dt>
-<dd><p class="first last">Write forces into the trajectory [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Write forces into the trajectory [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -409,15 +416,15 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
 </table>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRJ.NCDFWriter.is_periodic">
-<tt class="descname">is_periodic</tt><big>(</big><em>ts=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFWriter.is_periodic"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFWriter.is_periodic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Return <tt class="docutils literal"><span class="pre">True</span></tt> if <a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep" title="MDAnalysis.coordinates.TRJ.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> <em>ts</em> contains a valid simulation box</p>
+<code class="descname">is_periodic</code><span class="sig-paren">(</span><em>ts=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFWriter.is_periodic"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFWriter.is_periodic" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return <code class="docutils literal"><span class="pre">True</span></code> if <a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep" title="MDAnalysis.coordinates.TRJ.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> <em>ts</em> contains a valid simulation box</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRJ.NCDFWriter.write_next_timestep">
-<tt class="descname">write_next_timestep</tt><big>(</big><em>ts=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFWriter.write_next_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_next_timestep</code><span class="sig-paren">(</span><em>ts=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRJ.html#NCDFWriter.write_next_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRJ.NCDFWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>write a new timestep to the trj file</p>
-<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep" title="MDAnalysis.coordinates.TRJ.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance containing coordinates to
+<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.TRJ.Timestep" title="MDAnalysis.coordinates.TRJ.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance containing coordinates to
 be written to trajectory file</p>
 </dd></dl>
 
@@ -432,7 +439,7 @@ <h1>5.14. AMBER trajectories &#8212; <a class="reference internal" href="#module
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -447,11 +454,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="PQR.html" title="5.13. PQR file format — MDAnalysis.coordinates.PQR"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -461,7 +468,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
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     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/TRR.html b/package/doc/html/documentation_pages/coordinates/TRR.html
index 40dd065402b..f4e750169dc 100644
--- a/package/doc/html/documentation_pages/coordinates/TRR.html
+++ b/package/doc/html/documentation_pages/coordinates/TRR.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.15. Gromacs TRR file IO — MDAnalysis.coordinates.TRR &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.15. Gromacs TRR file IO — MDAnalysis.coordinates.TRR &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
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@@ -16,7 +14,7 @@
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+        VERSION:     '0.11.0',
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         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
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-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.16. Gromacs XTC file IO — MDAnalysis.coordinates.XTC" href="XTC.html" />
     <link rel="prev" title="5.14. AMBER trajectories — MDAnalysis.coordinates.TRJ" href="TRJ.html" /> 
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+    <div class="related" role="navigation" aria-label="related navigation">
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@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="TRJ.html" title="5.14. AMBER trajectories — MDAnalysis.coordinates.TRJ"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
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   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.15. Gromacs TRR file IO &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRR</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.15. Gromacs TRR file IO &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRR</span></code></a><ul>
 <li><a class="reference internal" href="#tips-and-tricks">5.15.1. Tips and Tricks</a><ul>
 <li><a class="reference internal" href="#filling-a-trr-with-pca-modes">5.15.1.1. Filling a TRR with PCA modes</a></li>
 </ul>
@@ -74,16 +72,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
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   <p class="topless"><a href="TRJ.html"
-                        title="previous chapter">5.14. AMBER trajectories &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></tt></a></p>
+                        title="previous chapter">5.14. AMBER trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></code></a></p>
   <h4>Next topic</h4>
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-  <h3>This Page</h3>
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-  </ul>
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+                        title="next chapter">5.16. Gromacs XTC file IO &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
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   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -102,37 +102,38 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.TRR"></span><div class="section" id="gromacs-trr-file-io-mdanalysis-coordinates-trr">
-<h1>5.15. Gromacs TRR file IO &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.TRR" title="MDAnalysis.coordinates.TRR"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRR</span></tt></a><a class="headerlink" href="#gromacs-trr-file-io-mdanalysis-coordinates-trr" title="Permalink to this headline">¶</a></h1>
+<h1>5.15. Gromacs TRR file IO &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.TRR" title="MDAnalysis.coordinates.TRR"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRR</span></code></a><a class="headerlink" href="#gromacs-trr-file-io-mdanalysis-coordinates-trr" title="Permalink to this headline">¶</a></h1>
 <p>The Gromacs <a class="reference external" href="http://www.gromacs.org/Documentation/File_Formats/.trr_File">TRR trajectory format</a> is a lossless format like
-e.g. the DCD format (see <a class="reference internal" href="DCD.html#module-MDAnalysis.coordinates.DCD" title="MDAnalysis.coordinates.DCD"><tt class="xref py py-mod docutils literal"><span class="pre">DCD</span></tt></a>) and
-unlike the <a class="reference internal" href="XTC.html#module-MDAnalysis.coordinates.XTC" title="MDAnalysis.coordinates.XTC"><tt class="xref py py-mod docutils literal"><span class="pre">XTC</span></tt></a> format, which stores
+e.g. the DCD format (see <a class="reference internal" href="DCD.html#module-MDAnalysis.coordinates.DCD" title="MDAnalysis.coordinates.DCD"><code class="xref py py-mod docutils literal"><span class="pre">DCD</span></code></a>) and
+unlike the <a class="reference internal" href="XTC.html#module-MDAnalysis.coordinates.XTC" title="MDAnalysis.coordinates.XTC"><code class="xref py py-mod docutils literal"><span class="pre">XTC</span></code></a> format, which stores
 reduced precision coordinates. Therefore, if one wants to convert
 <em>to</em> Gromacs trajectories without loss of precision then one should
 use the TRR format.</p>
 <p>The TRR format can store <em>velocities</em> and <em>forces</em> in addition to
 coordinates. It is also used by other Gromacs tools to store and
 process other data such as modes from a principal component analysis.</p>
-<p>The TRR I/O interface uses <a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt></a>
+<p>The TRR I/O interface uses <a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code></a>
 to implement random access to frames. This works by initially building an
 internal index of all frames and then using this index for direct
 seeks. Building the index is triggered by
-<a class="reference internal" href="xdrfile/libxdrfile2.html#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_n_frames" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_n_frames"><tt class="xref py py-func docutils literal"><span class="pre">read_trr_n_frames()</span></tt></a>, which
-typically happens when one accesses the <a class="reference internal" href="#MDAnalysis.coordinates.TRR.TRRReader.n_frames" title="MDAnalysis.coordinates.TRR.TRRReader.n_frames"><tt class="xref py py-attr docutils literal"><span class="pre">TRRReader.n_frames</span></tt></a> attribute
+<a class="reference internal" href="xdrfile/libxdrfile2.html#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_n_frames" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_n_frames"><code class="xref py py-func docutils literal"><span class="pre">read_trr_n_frames()</span></code></a>, which
+typically happens when one accesses the <a class="reference internal" href="#MDAnalysis.coordinates.TRR.TRRReader.n_frames" title="MDAnalysis.coordinates.TRR.TRRReader.n_frames"><code class="xref py py-attr docutils literal"><span class="pre">TRRReader.n_frames</span></code></a> attribute
 for the first time. Building the index may take many minutes for large
 trajectories but afterwards access is faster than with native Gromacs tools.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span>The TRR I/O interface now uses
-<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt></a>, which has seeking and
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span>The TRR I/O interface now uses
+<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code></a>, which has seeking and
 indexing capabilities. Note that unlike
-<tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></tt> before it,
-<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt></a> is distributed under the
+<code class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></code> before it,
+<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code></a> is distributed under the
 GNU GENERAL PUBLIC LICENSE, version 2 (or higher).
-<a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> now correctly deals
+<a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> now correctly deals
 with presence/absence of coordinate/velocity/force information on a
 per-frame basis.</p>
+</div>
 <div class="section" id="tips-and-tricks">
 <h2>5.15.1. Tips and Tricks<a class="headerlink" href="#tips-and-tricks" title="Permalink to this headline">¶</a></h2>
 <div class="section" id="filling-a-trr-with-pca-modes">
@@ -140,22 +141,22 @@ <h3>5.15.1.1. Filling a TRR with PCA modes<a class="headerlink" href="#filling-a
 <p>The following <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/79">recipe by Ramon Crehuet</a> shows how to convert modes
 stored in a NumPy-like array (e.g. from a PCA analysis with <a class="reference external" href="http://dirac.cnrs-orleans.fr/Manuals/MMTK/index.html">MMTK</a>) to
 a TRR usable by Gromacs. The idea is to manually fill a
-<a class="reference internal" href="xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> with the desired
+<a class="reference internal" href="xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> with the desired
 values and then write it to a file with the appropriate
-<a class="reference internal" href="xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter" title="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter"><tt class="xref py py-class docutils literal"><span class="pre">TRRWriter</span></tt></a>. In order to
+<a class="reference internal" href="xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter" title="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter"><code class="xref py py-class docutils literal"><span class="pre">TRRWriter</span></code></a>. In order to
 respect the Gromacs format for modes in a TRR file, one must write the
 average coordinates in the first frame of the TRR and the modes into
 subsequent ones. The mode number is stored in the
-<tt class="xref py py-attr docutils literal"><span class="pre">step</span></tt> attribute
+<code class="xref py py-attr docutils literal"><span class="pre">step</span></code> attribute
 and the mode coordinates are filling the
-<tt class="xref py py-attr docutils literal"><span class="pre">positions</span></tt> attribute of
-<a class="reference internal" href="xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>:</p>
-<div class="highlight-python"><pre># 'modes' is a mode object with M PCs, similar to a MxNx3 array
-# 'xav' the average coordinates, a Nx3 array for N atoms
+<code class="xref py py-attr docutils literal"><span class="pre">positions</span></code> attribute of
+<a class="reference internal" href="xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>:</p>
+<div class="highlight-python"><div class="highlight"><pre># &#39;modes&#39; is a mode object with M PCs, similar to a MxNx3 array
+# &#39;xav&#39; the average coordinates, a Nx3 array for N atoms
 
 N = len(xav)   # number of atoms, i.e. number of coordinates
 
-W = Writer('pca.trr', n_atoms=N)            # TRR writer
+W = Writer(&#39;pca.trr&#39;, n_atoms=N)            # TRR writer
 ts = MDAnalysis.coordinates.TRR.Timestep(N)  # TRR time step
                                              # N of atoms is passed.
 for frame,mode in enumerate(modes[4:16]):
@@ -174,7 +175,8 @@ <h3>5.15.1.1. Filling a TRR with PCA modes<a class="headerlink" href="#filling-a
        ts.time = mode.frequency
     W.write(ts)             # converts angstrom to nm for gmx
 
- W.close()</pre>
+ W.close()
+</pre></div>
 </div>
 </div>
 </div>
@@ -182,7 +184,7 @@ <h3>5.15.1.1. Filling a TRR with PCA modes<a class="headerlink" href="#filling-a
 <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.TRR.Timestep">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRR.</tt><tt class="descname">Timestep</tt><big>(</big><em>n_atoms</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRR.</code><code class="descname">Timestep</code><span class="sig-paren">(</span><em>n_atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/xdrfile/TRR.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Timestep for a <a class="reference external" href="http://www.gromacs.org">Gromacs</a> TRR trajectory.</p>
 <p>TRR Timestep always has positions, velocities and forces allocated, meaning
 that the <cite>_pos</cite>, <cite>_velocities</cite> and <cite>_forces</cite> attributes will always exist.
@@ -191,9 +193,9 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 by the entries in the data dictionary: <cite>position_source</cite>, <cite>velocity_source</cite>
 and <cite>force_source</cite>.
 When accessing the <cite>.positions</cite> attribute, this will only be returned if
-<cite>position_source</cite> matches the current <cite>frame</cite>, otherwise a <tt class="xref py py-class docutils literal"><span class="pre">NoDataError</span></tt>
+<cite>position_source</cite> matches the current <cite>frame</cite>, otherwise a <code class="xref py py-class docutils literal"><span class="pre">NoDataError</span></code>
 will be raised.  This scheme applies to both velocities and forces.</p>
-<p>When writing to the Timestep, it is important that the <tt class="xref py py-attr docutils literal"><span class="pre">frame</span></tt>
+<p>When writing to the Timestep, it is important that the <code class="xref py py-attr docutils literal"><span class="pre">frame</span></code>
 attribute is updated first!  This is because the source of the data is
 taken as the current frame of the Timestep.</p>
 <p>For example:</p>
@@ -212,34 +214,36 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
               <span class="c"># velocities was populated</span>
 </pre></div>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span>TRR <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects are now fully aware of the existence or
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span>TRR <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects are now fully aware of the existence or
 not of coordinate/velocity/force information in frames.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Velocities and forces can now be directly accessed via the <cite>velocities</cite> and
-<cite>forces</cite> attributes, with a <tt class="xref py py-class docutils literal"><span class="pre">NoDataError</span></tt> being raised
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Velocities and forces can now be directly accessed via the <cite>velocities</cite> and
+<cite>forces</cite> attributes, with a <code class="xref py py-class docutils literal"><span class="pre">NoDataError</span></code> being raised
 if no data was given for that frame.
 Management redone to use <cite>has_positions</cite>, <cite>has_velocities</cite> and
 <cite>has_forces</cite>.  Setting these will update the data dictionary entries
 which track the data.
 Timestep lmbda now stored in the data dictionary </p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.Timestep.copy">
-<tt class="descname">copy</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.copy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>.</p>
+<code class="descname">copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.Timestep.copy_slice">
-<tt class="descname">copy_slice</tt><big>(</big><em>sel</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
+<code class="descname">copy_slice</code><span class="sig-paren">(</span><em>sel</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy_slice"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
 <dd><p>Make a new Timestep containing a subset of the original Timestep.</p>
-<p><tt class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></tt>
-<tt class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></tt></p>
+<p><code class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></code>
+<code class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></code></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A Timestep object of the same type containing all header
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A Timestep object of the same type containing all header
 information and all atom information relevant to the selection.</td>
 </tr>
 </tbody>
@@ -249,16 +253,18 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 <p class="last">The selection must be a 0 based slice or array of the atom indices
 in this Timestep</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
 copy official attributes of the Timestep.</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.Timestep.dimensions">
-<tt class="descname">dimensions</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>unitcell dimensions (A, B, C, alpha, beta, gamma)</p>
 <ul class="simple">
 <li>A, B, C are the lengths of the primitive cell vectors e1, e2, e3</li>
@@ -270,43 +276,47 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.Timestep.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.dt" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dt</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.dt" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time difference in ps between timesteps</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">This defaults to 1.0 ps in the absence of time data</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
-<dl class="classmethod">
+<dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.Timestep.from_coordinates">
-<em class="property">classmethod </em><tt class="descname">from_coordinates</tt><big>(</big><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
+<code class="descname">from_coordinates</code><span class="sig-paren">(</span><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_coordinates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create an instance of this Timestep, from coordinate data</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
-<dl class="classmethod">
+<dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.Timestep.from_timestep">
-<em class="property">classmethod </em><tt class="descname">from_timestep</tt><big>(</big><em>other</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">from_timestep</code><span class="sig-paren">(</span><em>other</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a copy of another Timestep, in the format of this Timestep</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.Timestep.n_atoms">
-<tt class="descname">n_atoms</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>A read only view of the number of atoms this Timestep has</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.Timestep.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time in ps of this timestep</p>
 <p>This is calculated as:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">time</span>
@@ -316,19 +326,20 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span> <span class="o">*</span> <span class="n">ts</span><span class="o">.</span><span class="n">dt</span>
 </pre></div>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.Timestep.triclinic_dimensions">
-<tt class="descname">triclinic_dimensions</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">triclinic_dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>The unitcell dimensions represented as triclinic vectors</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
 </tr>
 </tbody>
 </table>
@@ -348,17 +359,18 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 <span class="go">        72.45159912,  71.56504822], dtype=float32)</span>
 </pre></div>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.Timestep.volume">
-<tt class="descname">volume</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.volume" title="Permalink to this definition">¶</a></dt>
+<code class="descname">volume</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.Timestep.volume" title="Permalink to this definition">¶</a></dt>
 <dd><p>volume of the unitcell</p>
 </dd></dl>
 
@@ -366,29 +378,31 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRR.</tt><tt class="descname">TRRReader</tt><big>(</big><em>filename</em>, <em>sub=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRR.</code><code class="descname">TRRReader</code><span class="sig-paren">(</span><em>filename</em>, <em>sub=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/xdrfile/TRR.html#TRRReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read a <a class="reference external" href="http://www.gromacs.org">Gromacs</a> TRR trajectory.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span><a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects returned from TRR files now have
-<tt class="xref py py-attr docutils literal"><span class="pre">has_x</span></tt>, <tt class="xref py py-attr docutils literal"><span class="pre">has_velocities</span></tt>, and <tt class="xref py py-attr docutils literal"><span class="pre">has_forces</span></tt>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span><a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects returned from TRR files now have
+<code class="xref py py-attr docutils literal"><span class="pre">has_x</span></code>, <code class="xref py py-attr docutils literal"><span class="pre">has_velocities</span></code>, and <code class="xref py py-attr docutils literal"><span class="pre">has_forces</span></code>
 flags reflecting whether coordinates/velocities/forces were read.
-Attempting to access such data when the corresponding flag is set to <tt class="docutils literal"><span class="pre">False</span></tt>
-will raise a <tt class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></tt>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Returned Timesteps will always be a <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance.
+Attempting to access such data when the corresponding flag is set to <code class="docutils literal"><span class="pre">False</span></code>
+will raise a <code class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></code>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Returned Timesteps will always be a <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance.
 Attributes lmbda and status now stored in the TS.data dictionary</p>
+</div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">the name of the trr file.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>sub</em></dt>
 <dd><p class="first">an numpy integer array of what subset of trajectory atoms to load into
 the timestep. Intended to work similarly to the &#8216;sub&#8217; argument to <a class="reference external" href="http://www.gromacs.org">Gromacs</a>&#8216; trjconv.</p>
@@ -398,47 +412,50 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 equal to number of atoms in the Universe.</p>
 </dd>
 <dt><em>refresh_offsets</em></dt>
-<dd><p class="first last">if <tt class="docutils literal"><span class="pre">True</span></tt>, do not retrieve stored offsets, but instead generate
-new ones; if <tt class="docutils literal"><span class="pre">False</span></tt>, use retrieved offsets if available [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">if <code class="docutils literal"><span class="pre">True</span></code>, do not retrieve stored offsets, but instead generate
+new ones; if <code class="docutils literal"><span class="pre">False</span></code>, use retrieved offsets if available [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>refresh_offsets</em></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Renamed &#8220;delta&#8221; attribute to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>refresh_offsets</em></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Renamed &#8220;delta&#8221; attribute to &#8220;dt&#8221;
+Now passes weakref of self to ts (as &#8220;_reader&#8221;)</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.OtherWriter">
-<tt class="descname">OtherWriter</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">OtherWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a writer appropriate for <em>filename</em>.</p>
 <p>Sets the default keywords <em>start</em>, <em>step</em> and <em>dt</em> (if
-available). <em>n_atoms</em> is always set from <tt class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></tt>.</p>
-<div class="admonition-see-also admonition seealso">
+available). <em>n_atoms</em> is always set from <code class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></code>.</p>
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></tt> and <tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></tt></p>
+<p class="last"><code class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></code> and <code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a Gromacs TrjWriter for <em>filename</em> with the same parameters as this trajectory.</p>
 <p>All values can be changed through keyword arguments.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">number of atoms</p>
 </dd>
@@ -452,132 +469,139 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">appropriate <tt class="xref py py-class docutils literal"><span class="pre">TrjWriter</span></tt></p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">appropriate <code class="xref py py-class docutils literal"><span class="pre">TrjWriter</span></code></p>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Changed &#8220;delta&#8221; keyword to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Changed &#8220;delta&#8221; keyword to &#8220;dt&#8221;</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close xdr trajectory file if it was open.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.dt" title="Permalink to this definition">¶</a></dt>
-<dd><p>Time step length in ps.</p>
-<p>The result is computed from the trajectory and cached. If for
-any reason the trajectory cannot be read then 0 is returned.</p>
+<code class="descname">dt</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.dt" title="Permalink to this definition">¶</a></dt>
+<dd><p>Time between two trajectory frames in picoseconds.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.frame">
-<tt class="descname">frame</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.frame" title="Permalink to this definition">¶</a></dt>
+<code class="descname">frame</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.frame" title="Permalink to this definition">¶</a></dt>
 <dd><p>Frame number of the current time step.</p>
-<p>This is a simple short cut to <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt>.</p>
+<p>This is a simple short cut to <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.load_offsets">
-<tt class="descname">load_offsets</tt><big>(</big><em>filename</em>, <em>check=False</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.load_offsets" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_offsets</code><span class="sig-paren">(</span><em>filename</em>, <em>check=False</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.load_offsets" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads current trajectory offsets from pickled <em>filename</em>.</p>
 <p>Checks if ctime and size of trajectory file matches that stored in
-pickled <em>filename</em>.  If either one does not match (and <em>check</em> == <tt class="docutils literal"><span class="pre">True</span></tt>)
+pickled <em>filename</em>.  If either one does not match (and <em>check</em> == <code class="docutils literal"><span class="pre">True</span></code>)
 then the offsets are not loaded.  This is intended to conservatively
 avoid loading out-of-date offsets.</p>
 <dl class="docutils">
@@ -596,22 +620,22 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
-<dd><p class="first last">filename of pickle file saved with <tt class="xref py py-meth docutils literal"><span class="pre">save_offsets()</span></tt> 
+<dd><p class="first last">filename of pickle file saved with <code class="xref py py-meth docutils literal"><span class="pre">save_offsets()</span></code> 
 with the frame offsets for the loaded trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>check</em></dt>
 <dd><p class="first last">if False, ignore ctime and size check of trajectory file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> if the file cannot be read (see <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">open()</span></tt></a>).</p>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> if the file cannot be read (see <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">open()</span></code></a>).</p>
 </td>
 </tr>
 </tbody>
@@ -620,7 +644,7 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.n_atoms">
-<tt class="descname">n_atoms</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>The number of publically available atoms that this reader will store in the timestep.</p>
 <p>If &#8216;sub&#8217; was not given in the ctor, then this value will just be the actual
 number of atoms in the underlying trajectory file. If however &#8216;sub&#8217; was given, then
@@ -630,7 +654,7 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.n_frames">
-<tt class="descname">n_frames</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.n_frames" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_frames</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.n_frames" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the number of frames from the trajectory.</p>
 <p>The result is cached. If for any reason the trajectory cannot
 be read then 0 is returned.</p>
@@ -638,29 +662,29 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 iterating through the whole trajectory. If the trajectory
 was previously loaded and saved offsets exist, then
 loading will be significantly faster.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-meth docutils literal"><span class="pre">TrjReader.load_offsets()</span></tt> and <tt class="xref py py-meth docutils literal"><span class="pre">TrjReader.save_offsets()</span></tt></p>
+<p class="last"><code class="xref py py-meth docutils literal"><span class="pre">TrjReader.load_offsets()</span></code> and <code class="xref py py-meth docutils literal"><span class="pre">TrjReader.save_offsets()</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.next">
-<tt class="descname">next</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.next" title="Permalink to this definition">¶</a></dt>
+<code class="descname">next</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.next" title="Permalink to this definition">¶</a></dt>
 <dd><p>Forward one step to next frame.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.open_trajectory">
-<tt class="descname">open_trajectory</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
+<code class="descname">open_trajectory</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
 <dd><p>Open xdr trajectory file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">pointer to XDRFILE (and sets self.xdrfile)</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">pointer to XDRFILE (and sets self.xdrfile)</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> with code EALREADY if file was already opened or
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> with code EALREADY if file was already opened or
 ENOENT if the file cannot be found</td>
 </tr>
 </tbody>
@@ -669,13 +693,13 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.rewind">
-<tt class="descname">rewind</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.rewind" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rewind</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.rewind" title="Permalink to this definition">¶</a></dt>
 <dd><p>Position at beginning of trajectory</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.save_offsets">
-<tt class="descname">save_offsets</tt><big>(</big><em>filename</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.save_offsets" title="Permalink to this definition">¶</a></dt>
+<code class="descname">save_offsets</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.save_offsets" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves current trajectory offsets into <em>filename</em>, as a pickled object.</p>
 <p>Along with the offsets themselves, the ctime and file size of the
 trajectory file are also saved.  These are used upon load as a check to
@@ -697,7 +721,7 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename in which to save the frame offsets</p>
 </dd>
@@ -710,15 +734,15 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>Time of the current frame in MDAnalysis time units (typically ps).</p>
 <p>This is either read straight from the Timestep, or calculated as
-time = <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt> * <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep.dt" title="MDAnalysis.coordinates.TRR.Timestep.dt"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></tt></a></p>
+time = <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code> * <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep.dt" title="MDAnalysis.coordinates.TRR.Timestep.dt"><code class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></code></a></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRR.TRRReader.totaltime">
-<tt class="descname">totaltime</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.totaltime" title="Permalink to this definition">¶</a></dt>
+<code class="descname">totaltime</code><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRReader.totaltime" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total length of the trajectory n_frames * dt.</p>
 </dd></dl>
 
@@ -726,14 +750,14 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRR.</tt><tt class="descname">TRRWriter</tt><big>(</big><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=None</em>, <em>precision=1000.0</em>, <em>remarks=None</em>, <em>convert_units=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRR.</code><code class="descname">TRRWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=None</em>, <em>precision=1000.0</em>, <em>remarks=None</em>, <em>convert_units=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/xdrfile/TRR.html#TRRWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a <a class="reference external" href="http://www.gromacs.org">Gromacs</a> TRR trajectory.</p>
 <p>Create a new TrjWriter</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of output file</p>
 </dd>
@@ -743,7 +767,7 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>start</em></dt>
 <dd><p class="first last">starting timestep frame; only used when <em>dt</em> is set.</p>
 </dd>
@@ -752,9 +776,9 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 </dd>
 <dt><em>dt</em></dt>
 <dd><p class="first last">time between frames to use. If set will override any time information
-contained in the passed <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects, which will otherwise
+contained in the passed <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects, which will otherwise
 be used.
-The <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep.time" title="MDAnalysis.coordinates.TRR.Timestep.time"><tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt></a> attribute defaults to a timestep of
+The <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep.time" title="MDAnalysis.coordinates.TRR.Timestep.time"><code class="xref py py-attr docutils literal"><span class="pre">time</span></code></a> attribute defaults to a timestep of
 to setting the trajectory time at 1 ps per step if there is no
 time information.</p>
 </dd>
@@ -763,121 +787,131 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 for TRR) [1000.0]</p>
 </dd>
 <dt><em>convert_units</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: units are converted to the MDAnalysis base format; <tt class="docutils literal"><span class="pre">None</span></tt> selects
-the value of <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> [&#8216;convert_lengths&#8217;].
-(see <a class="reference internal" href="../core/init.html#flags-label"><em>Flags</em></a>)</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: units are converted to the MDAnalysis base format; <code class="docutils literal"><span class="pre">None</span></code> selects
+the value of <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> [&#8216;convert_lengths&#8217;].
+(see <a class="reference internal" href="../core/init.html#flags-label"><span>Flags</span></a>)</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span>The TRR writer is now able to write TRRs without coordinates/velocities/forces,
-depending on the properties available in the <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects passed to
-<a class="reference internal" href="#MDAnalysis.coordinates.TRR.TRRWriter.write" title="MDAnalysis.coordinates.TRR.TRRWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Keyword &#8220;delta&#8221; renamed to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span>The TRR writer is now able to write TRRs without coordinates/velocities/forces,
+depending on the properties available in the <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects passed to
+<a class="reference internal" href="#MDAnalysis.coordinates.TRR.TRRWriter.write" title="MDAnalysis.coordinates.TRR.TRRWriter.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Keyword &#8220;delta&#8221; renamed to &#8220;dt&#8221;</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.convert_dimensions_to_unitcell">
-<tt class="descname">convert_dimensions_to_unitcell</tt><big>(</big><em>ts</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_dimensions_to_unitcell</code><span class="sig-paren">(</span><em>ts</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read dimensions from timestep <em>ts</em> and return Gromacs box vectors</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.has_valid_coordinates">
-<tt class="descname">has_valid_coordinates</tt><big>(</big><em>criteria</em>, <em>x</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns <tt class="docutils literal"><span class="pre">True</span></tt> if all values are within limit values of their formats.</p>
+<code class="descname">has_valid_coordinates</code><span class="sig-paren">(</span><em>criteria</em>, <em>x</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns <code class="docutils literal"><span class="pre">True</span></code> if all values are within limit values of their formats.</p>
 <p>Due to rounding, the test is asymmetric (and <em>min</em> is supposed to be negative):</p>
 <blockquote>
 <div>min &lt; x &lt;= max</div></blockquote>
@@ -885,17 +919,17 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>criteria</em></dt>
 <dd><p class="first last">dictionary containing the <em>max</em> and <em>min</em> values in native units</p>
 </dd>
 <dt><em>x</em></dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></tt> of <tt class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></tt> coordinates of atoms selected to be written out.</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></code> of <code class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></code> coordinates of atoms selected to be written out.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">boolean</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">boolean</p>
 </td>
 </tr>
 </tbody>
@@ -904,10 +938,10 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.write">
-<tt class="descname">write</tt><big>(</big><em>obj</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write current timestep, using the supplied <em>obj</em>.</p>
-<p>The argument should be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> or
-a <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> or a <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance.</p>
+<p>The argument should be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> or
+a <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> or a <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The size of the <em>obj</em> must be the same as the number of atom
@@ -917,9 +951,9 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRR.TRRWriter.write_next_timestep">
-<tt class="descname">write_next_timestep</tt><big>(</big><em>ts=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_next_timestep</code><span class="sig-paren">(</span><em>ts=None</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.TRR.TRRWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>write a new timestep to the trj file</p>
-<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance containing coordinates to
+<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.TRR.Timestep" title="MDAnalysis.coordinates.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance containing coordinates to
 be written to trajectory file</p>
 </dd></dl>
 
@@ -934,7 +968,7 @@ <h2>5.15.2. Module reference<a class="headerlink" href="#module-reference" title
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -949,11 +983,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="TRJ.html" title="5.14. AMBER trajectories — MDAnalysis.coordinates.TRJ"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -963,7 +997,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/TRZ.html b/package/doc/html/documentation_pages/coordinates/TRZ.html
index 7241167e2f7..c5535503b3e 100644
--- a/package/doc/html/documentation_pages/coordinates/TRZ.html
+++ b/package/doc/html/documentation_pages/coordinates/TRZ.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.18. TRZ trajectory I/O — MDAnalysis.coordinates.TRZ &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.18. TRZ trajectory I/O — MDAnalysis.coordinates.TRZ &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.19. Base classes — MDAnalysis.coordinates.base" href="base.html" />
     <link rel="prev" title="5.17. XYZ trajectory reader — MDAnalysis.coordinates.XYZ" href="XYZ.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="XYZ.html" title="5.17. XYZ trajectory reader — MDAnalysis.coordinates.XYZ"
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+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
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+                        title="previous chapter">5.17. XYZ trajectory reader &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.XYZ</span></code></a></p>
   <h4>Next topic</h4>
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-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/TRZ.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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+                        title="next chapter">5.19. Base classes &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
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+      <li><a href="../../_sources/documentation_pages/coordinates/TRZ.txt"
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   <h3>Quick search</h3>
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-          <div class="body">
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   <span class="target" id="module-MDAnalysis.coordinates.TRZ"></span><div class="section" id="trz-trajectory-i-o-mdanalysis-coordinates-trz">
-<h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.TRZ" title="MDAnalysis.coordinates.TRZ"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRZ</span></tt></a><a class="headerlink" href="#trz-trajectory-i-o-mdanalysis-coordinates-trz" title="Permalink to this headline">¶</a></h1>
+<h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.TRZ" title="MDAnalysis.coordinates.TRZ"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRZ</span></code></a><a class="headerlink" href="#trz-trajectory-i-o-mdanalysis-coordinates-trz" title="Permalink to this headline">¶</a></h1>
 <p>Classes to read <a class="reference external" href="http://www.theo.chemie.tu-darmstadt.de/ibisco/IBISCO.html">IBIsCO</a> / <a class="reference external" href="http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html">YASP</a> binary trajectories.</p>
 <p>Reads coordinates, velocities and more (see attributes of the
-<a class="reference internal" href="#MDAnalysis.coordinates.TRZ.Timestep" title="MDAnalysis.coordinates.TRZ.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>).</p>
+<a class="reference internal" href="#MDAnalysis.coordinates.TRZ.Timestep" title="MDAnalysis.coordinates.TRZ.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>).</p>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.TRZ.Timestep">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRZ.</tt><tt class="descname">Timestep</tt><big>(</big><em>n_atoms</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRZ.</code><code class="descname">Timestep</code><span class="sig-paren">(</span><em>n_atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>TRZ custom Timestep</p>
 <p>Create a Timestep, representing a frame of a trajectory</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">The total number of atoms this Timestep describes</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>positions</em></dt>
-<dd><p class="first last">Whether this Timestep has position information [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has position information [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 <dt><em>velocities</em></dt>
-<dd><p class="first last">Whether this Timestep has velocity information [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has velocity information [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>forces</em></dt>
-<dd><p class="first last">Whether this Timestep has force information [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has force information [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>dt</em></dt>
-<dd><p class="first last">The time difference between frames (ps).  If <a class="reference internal" href="#MDAnalysis.coordinates.TRZ.Timestep.time" title="MDAnalysis.coordinates.TRZ.Timestep.time"><tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt></a>
+<dd><p class="first last">The time difference between frames (ps).  If <a class="reference internal" href="#MDAnalysis.coordinates.TRZ.Timestep.time" title="MDAnalysis.coordinates.TRZ.Timestep.time"><code class="xref py py-attr docutils literal"><span class="pre">time</span></code></a>
 is set, then <cite>dt</cite> will be ignored.</p>
 </dd>
 <dt><em>time_offset</em></dt>
@@ -135,99 +135,100 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Added keywords for positions, velocities and forces
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Added keywords for positions, velocities and forces
 Can add and remove position/velocity/force information by using
 the has_* attribute</p>
+</div>
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.Timestep.frame">
-<tt class="descname">frame</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.frame" title="Permalink to this definition">¶</a></dt>
+<code class="descname">frame</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.frame" title="Permalink to this definition">¶</a></dt>
 <dd><p>Index of current frame number (0 based)</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.Timestep.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>Current system time in ps</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.Timestep.n_atoms">
-<tt class="descname">n_atoms</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Number of atoms in the frame (will be constant throughout trajectory)</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.Timestep.pressure">
-<tt class="descname">pressure</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.pressure" title="Permalink to this definition">¶</a></dt>
+<code class="descname">pressure</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.pressure" title="Permalink to this definition">¶</a></dt>
 <dd><p>System pressure in pascals</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.Timestep.pressure_tensor">
-<tt class="descname">pressure_tensor</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.pressure_tensor" title="Permalink to this definition">¶</a></dt>
+<code class="descname">pressure_tensor</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.pressure_tensor" title="Permalink to this definition">¶</a></dt>
 <dd><p>Array containing pressure tensors in order: xx, xy, yy, xz, yz, zz</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.Timestep.total_energy">
-<tt class="descname">total_energy</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.total_energy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">total_energy</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.total_energy" title="Permalink to this definition">¶</a></dt>
 <dd><p>Hamiltonian for the system in kJ/mol</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.Timestep.potential_energy">
-<tt class="descname">potential_energy</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.potential_energy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">potential_energy</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.potential_energy" title="Permalink to this definition">¶</a></dt>
 <dd><p>Potential energy of the system in kJ/mol</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.Timestep.kinetic_energy">
-<tt class="descname">kinetic_energy</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.kinetic_energy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">kinetic_energy</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.kinetic_energy" title="Permalink to this definition">¶</a></dt>
 <dd><p>Kinetic energy of the system in kJ/mol</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.Timestep.temperature">
-<tt class="descname">temperature</tt><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.temperature" title="Permalink to this definition">¶</a></dt>
+<code class="descname">temperature</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.temperature" title="Permalink to this definition">¶</a></dt>
 <dd><p>Temperature of the system in Kelvin</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.Timestep.dimensions">
-<tt class="descname">dimensions</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#Timestep.dimensions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
-<dd><p>Unit cell dimensions <tt class="docutils literal"><span class="pre">[A,B,C,alpha,beta,gamma]</span></tt>.</p>
+<code class="descname">dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
+<dd><p>Unit cell dimensions <code class="docutils literal"><span class="pre">[A,B,C,alpha,beta,gamma]</span></code>.</p>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.TRZ.TRZReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRZ.</tt><tt class="descname">TRZReader</tt><big>(</big><em>trzfilename</em>, <em>n_atoms=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRZ.</code><code class="descname">TRZReader</code><span class="sig-paren">(</span><em>trzfilename</em>, <em>n_atoms=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reads an IBIsCO or YASP trajectory file</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Data :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Data:</th><td class="field-body"><dl class="first docutils">
 <dt>ts</dt>
-<dd><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.TRZ.Timestep" title="MDAnalysis.coordinates.TRZ.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> object
+<dd><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.TRZ.Timestep" title="MDAnalysis.coordinates.TRZ.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> object
 containing coordinates of current frame</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Methods :</th><td class="field-body"><dl class="first last docutils">
-<dt><tt class="docutils literal"><span class="pre">len(trz)</span></tt></dt>
+<tr class="field-even field"><th class="field-name">Methods:</th><td class="field-body"><dl class="first last docutils">
+<dt><code class="docutils literal"><span class="pre">len(trz)</span></code></dt>
 <dd><p class="first last">returns the number of frames</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">trz</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">trz</span></code></dt>
 <dd><p class="first last">iterates through the trajectory</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">trz[start:stop:skip]</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">trz[start:stop:skip]</span></code></dt>
 <dd><p class="first last">iterate through a trajectory using slicing</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">trz[i]</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">trz[i]</span></code></dt>
 <dd><p class="first last">random access of a trajectory frame</p>
 </dd>
 </dl>
@@ -235,16 +236,18 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based
 Extra data (Temperature, Energies, Pressures, etc) now read
-into ts.data dictionary</p>
+into ts.data dictionary
+Now passes a weakref of self to ts (ts._reader)</p>
+</div>
 <p>Creates a TRZ Reader</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>trzfilename</em></dt>
 <dd><p class="first last">name of input file</p>
 </dd>
@@ -261,46 +264,37 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 </table>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRZ.TRZReader.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close trz file if it was open</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.TRZReader.delta">
-<tt class="descname">delta</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.delta"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.delta" title="Permalink to this definition">¶</a></dt>
+<code class="descname">delta</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.delta" title="Permalink to this definition">¶</a></dt>
 <dd><p>MD integration timestep</p>
 </dd></dl>
 
-<dl class="attribute">
-<dt id="MDAnalysis.coordinates.TRZ.TRZReader.dt">
-<tt class="descname">dt</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.dt"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.dt" title="Permalink to this definition">¶</a></dt>
-<dd><p>The amount of time between frames in ps</p>
-<p>Assumes that this step is constant (ie. 2 trajectories with different steps haven&#8217;t been
-stitched together)
-Returns 0 in case of IOError</p>
-</dd></dl>
-
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.TRZReader.n_atoms">
-<tt class="descname">n_atoms</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.n_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Number of atoms in a frame</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.TRZReader.n_frames">
-<tt class="descname">n_frames</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.n_frames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.n_frames" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_frames</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.n_frames" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total number of frames in a trajectory</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRZ.TRZReader.open_trajectory">
-<tt class="descname">open_trajectory</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.open_trajectory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
+<code class="descname">open_trajectory</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.open_trajectory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
 <dd><p>Open the trajectory file</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.TRZ.TRZReader.skip_timestep">
-<tt class="descname">skip_timestep</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.skip_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.skip_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">skip_timestep</code><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZReader.skip_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Timesteps between trajectory frames</p>
 </dd></dl>
 
@@ -308,13 +302,13 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.TRZ.TRZWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRZ.</tt><tt class="descname">TRZWriter</tt><big>(</big><em>filename</em>, <em>n_atoms</em>, <em>title='TRZ'</em>, <em>convert_units=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRZ.</code><code class="descname">TRZWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms</em>, <em>title='TRZ'</em>, <em>convert_units=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Writes a TRZ format trajectory.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Methods :</th><td class="field-body"><tt class="docutils literal"><span class="pre">W</span> <span class="pre">=</span> <span class="pre">TRZWriter(trzfilename,</span> <span class="pre">n_atoms,</span> <span class="pre">title='TRZ')</span></tt></td>
+<tr class="field-odd field"><th class="field-name">Methods:</th><td class="field-body"><code class="docutils literal"><span class="pre">W</span> <span class="pre">=</span> <span class="pre">TRZWriter(trzfilename,</span> <span class="pre">n_atoms,</span> <span class="pre">title='TRZ')</span></code></td>
 </tr>
 </tbody>
 </table>
@@ -323,7 +317,7 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of output file</p>
 </dd>
@@ -333,14 +327,14 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>title</em></dt>
 <dd><p class="first last">title of the trajectory</p>
 </dd>
 <dt><em>convert_units</em></dt>
-<dd><p class="first last">units are converted to the MDAnalysis base format; <tt class="docutils literal"><span class="pre">None</span></tt> selects
-the value of <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> [&#8216;convert_lengths&#8217;].
-(see <a class="reference internal" href="../core/init.html#flags-label"><em>Flags</em></a>)</p>
+<dd><p class="first last">units are converted to the MDAnalysis base format; <code class="docutils literal"><span class="pre">None</span></code> selects
+the value of <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> [&#8216;convert_lengths&#8217;].
+(see <a class="reference internal" href="../core/init.html#flags-label"><span>Flags</span></a>)</p>
 </dd>
 </dl>
 </td>
@@ -349,7 +343,7 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 </table>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.TRZ.TRZWriter.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZWriter.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZWriter.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZWriter.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.TRZ.TRZWriter.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close if it was open</p>
 </dd></dl>
 
@@ -357,31 +351,31 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 
 <dl class="class">
 <dt>
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRZ.</tt><tt class="descname">TRZReader</tt><big>(</big><em>trzfilename</em>, <em>n_atoms=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader"><span class="viewcode-link">[source]</span></a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRZ.</code><code class="descname">TRZReader</code><span class="sig-paren">(</span><em>trzfilename</em>, <em>n_atoms=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Reads an IBIsCO or YASP trajectory file</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Data :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Data:</th><td class="field-body"><dl class="first docutils">
 <dt>ts</dt>
-<dd><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.TRZ.Timestep" title="MDAnalysis.coordinates.TRZ.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> object
+<dd><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.TRZ.Timestep" title="MDAnalysis.coordinates.TRZ.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> object
 containing coordinates of current frame</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Methods :</th><td class="field-body"><dl class="first last docutils">
-<dt><tt class="docutils literal"><span class="pre">len(trz)</span></tt></dt>
+<tr class="field-even field"><th class="field-name">Methods:</th><td class="field-body"><dl class="first last docutils">
+<dt><code class="docutils literal"><span class="pre">len(trz)</span></code></dt>
 <dd><p class="first last">returns the number of frames</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">trz</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">trz</span></code></dt>
 <dd><p class="first last">iterates through the trajectory</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">trz[start:stop:skip]</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">trz[start:stop:skip]</span></code></dt>
 <dd><p class="first last">iterate through a trajectory using slicing</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">trz[i]</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">trz[i]</span></code></dt>
 <dd><p class="first last">random access of a trajectory frame</p>
 </dd>
 </dl>
@@ -389,16 +383,18 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based
 Extra data (Temperature, Energies, Pressures, etc) now read
-into ts.data dictionary</p>
+into ts.data dictionary
+Now passes a weakref of self to ts (ts._reader)</p>
+</div>
 <p>Creates a TRZ Reader</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>trzfilename</em></dt>
 <dd><p class="first last">name of input file</p>
 </dd>
@@ -415,46 +411,37 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 </table>
 <dl class="method">
 <dt>
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.close"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.close"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Close trz file if it was open</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt>
-<tt class="descname">delta</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.delta"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">delta</code></dt>
 <dd><p>MD integration timestep</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt>
-<tt class="descname">dt</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.dt"><span class="viewcode-link">[source]</span></a></dt>
-<dd><p>The amount of time between frames in ps</p>
-<p>Assumes that this step is constant (ie. 2 trajectories with different steps haven&#8217;t been
-stitched together)
-Returns 0 in case of IOError</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt>
-<tt class="descname">n_atoms</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.n_atoms"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">n_atoms</code></dt>
 <dd><p>Number of atoms in a frame</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt>
-<tt class="descname">n_frames</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.n_frames"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">n_frames</code></dt>
 <dd><p>Total number of frames in a trajectory</p>
 </dd></dl>
 
 <dl class="method">
 <dt>
-<tt class="descname">open_trajectory</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.open_trajectory"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">open_trajectory</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.open_trajectory"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Open the trajectory file</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt>
-<tt class="descname">skip_timestep</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZReader.skip_timestep"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">skip_timestep</code></dt>
 <dd><p>Timesteps between trajectory frames</p>
 </dd></dl>
 
@@ -462,13 +449,13 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 
 <dl class="class">
 <dt>
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRZ.</tt><tt class="descname">TRZWriter</tt><big>(</big><em>filename</em>, <em>n_atoms</em>, <em>title='TRZ'</em>, <em>convert_units=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZWriter"><span class="viewcode-link">[source]</span></a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRZ.</code><code class="descname">TRZWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms</em>, <em>title='TRZ'</em>, <em>convert_units=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZWriter"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Writes a TRZ format trajectory.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Methods :</th><td class="field-body"><tt class="docutils literal"><span class="pre">W</span> <span class="pre">=</span> <span class="pre">TRZWriter(trzfilename,</span> <span class="pre">n_atoms,</span> <span class="pre">title='TRZ')</span></tt></td>
+<tr class="field-odd field"><th class="field-name">Methods:</th><td class="field-body"><code class="docutils literal"><span class="pre">W</span> <span class="pre">=</span> <span class="pre">TRZWriter(trzfilename,</span> <span class="pre">n_atoms,</span> <span class="pre">title='TRZ')</span></code></td>
 </tr>
 </tbody>
 </table>
@@ -477,7 +464,7 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of output file</p>
 </dd>
@@ -487,14 +474,14 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>title</em></dt>
 <dd><p class="first last">title of the trajectory</p>
 </dd>
 <dt><em>convert_units</em></dt>
-<dd><p class="first last">units are converted to the MDAnalysis base format; <tt class="docutils literal"><span class="pre">None</span></tt> selects
-the value of <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> [&#8216;convert_lengths&#8217;].
-(see <a class="reference internal" href="../core/init.html#flags-label"><em>Flags</em></a>)</p>
+<dd><p class="first last">units are converted to the MDAnalysis base format; <code class="docutils literal"><span class="pre">None</span></code> selects
+the value of <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> [&#8216;convert_lengths&#8217;].
+(see <a class="reference internal" href="../core/init.html#flags-label"><span>Flags</span></a>)</p>
 </dd>
 </dl>
 </td>
@@ -503,7 +490,7 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 </table>
 <dl class="method">
 <dt>
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZWriter.close"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#TRZWriter.close"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Close if it was open</p>
 </dd></dl>
 
@@ -511,32 +498,32 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 
 <dl class="class">
 <dt>
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.TRZ.</tt><tt class="descname">Timestep</tt><big>(</big><em>n_atoms</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#Timestep"><span class="viewcode-link">[source]</span></a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.TRZ.</code><code class="descname">Timestep</code><span class="sig-paren">(</span><em>n_atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#Timestep"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>TRZ custom Timestep</p>
 <p>Create a Timestep, representing a frame of a trajectory</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">The total number of atoms this Timestep describes</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>positions</em></dt>
-<dd><p class="first last">Whether this Timestep has position information [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has position information [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 <dt><em>velocities</em></dt>
-<dd><p class="first last">Whether this Timestep has velocity information [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has velocity information [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>forces</em></dt>
-<dd><p class="first last">Whether this Timestep has force information [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has force information [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>dt</em></dt>
-<dd><p class="first last">The time difference between frames (ps).  If <a class="reference internal" href="#MDAnalysis.coordinates.TRZ.Timestep.time" title="MDAnalysis.coordinates.TRZ.Timestep.time"><tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt></a>
+<dd><p class="first last">The time difference between frames (ps).  If <a class="reference internal" href="#MDAnalysis.coordinates.TRZ.Timestep.time" title="MDAnalysis.coordinates.TRZ.Timestep.time"><code class="xref py py-attr docutils literal"><span class="pre">time</span></code></a>
 is set, then <cite>dt</cite> will be ignored.</p>
 </dd>
 <dt><em>time_offset</em></dt>
@@ -547,14 +534,15 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Added keywords for positions, velocities and forces
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Added keywords for positions, velocities and forces
 Can add and remove position/velocity/force information by using
 the has_* attribute</p>
+</div>
 <dl class="attribute">
 <dt>
-<tt class="descname">dimensions</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/TRZ.html#Timestep.dimensions"><span class="viewcode-link">[source]</span></a></dt>
-<dd><p>Unit cell dimensions <tt class="docutils literal"><span class="pre">[A,B,C,alpha,beta,gamma]</span></tt>.</p>
+<code class="descname">dimensions</code></dt>
+<dd><p>Unit cell dimensions <code class="docutils literal"><span class="pre">[A,B,C,alpha,beta,gamma]</span></code>.</p>
 </dd></dl>
 
 </dd></dl>
@@ -567,7 +555,7 @@ <h1>5.18. TRZ trajectory I/O  &#8212; <a class="reference internal" href="#modul
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -582,11 +570,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="XYZ.html" title="5.17. XYZ trajectory reader — MDAnalysis.coordinates.XYZ"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -596,7 +584,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/XTC.html b/package/doc/html/documentation_pages/coordinates/XTC.html
index 55fd2650aa7..6d5f469cafc 100644
--- a/package/doc/html/documentation_pages/coordinates/XTC.html
+++ b/package/doc/html/documentation_pages/coordinates/XTC.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
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+    <title>5.16. Gromacs XTC file IO — MDAnalysis.coordinates.XTC &mdash; MDAnalysis 0.11.0 documentation</title>
     
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@@ -27,16 +25,16 @@
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-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.17. XYZ trajectory reader — MDAnalysis.coordinates.XYZ" href="XYZ.html" />
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-<li><a class="reference internal" href="#">5.16. Gromacs XTC file IO &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.16. Gromacs XTC file IO &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></code></a><ul>
 <li><a class="reference internal" href="#module-reference">5.16.1. Module reference</a></li>
 </ul>
 </li>
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   <span class="target" id="module-MDAnalysis.coordinates.XTC"></span><div class="section" id="gromacs-xtc-file-io-mdanalysis-coordinates-xtc">
-<h1>5.16. Gromacs XTC file IO &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.XTC" title="MDAnalysis.coordinates.XTC"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></tt></a><a class="headerlink" href="#gromacs-xtc-file-io-mdanalysis-coordinates-xtc" title="Permalink to this headline">¶</a></h1>
+<h1>5.16. Gromacs XTC file IO &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.XTC" title="MDAnalysis.coordinates.XTC"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></code></a><a class="headerlink" href="#gromacs-xtc-file-io-mdanalysis-coordinates-xtc" title="Permalink to this headline">¶</a></h1>
 <p>The Gromacs <a class="reference external" href="http://www.gromacs.org/Documentation/File_Formats/.xtc_File">XTC trajectory format</a> is a format with lossy
 compression. Coordinates are only stored with a fixed precision (by
 default, 1/1000 of a nm). The XTC format can only store
@@ -110,53 +110,55 @@ <h1>5.16. Gromacs XTC file IO &#8212; <a class="reference internal" href="#modul
 not a problem.</p>
 <p>If one wants to store Gromacs trajectories without loss of precision
 or with velocities and/or forces then one should use the TRR format
-(see module <a class="reference internal" href="TRR.html#module-MDAnalysis.coordinates.TRR" title="MDAnalysis.coordinates.TRR"><tt class="xref py py-mod docutils literal"><span class="pre">TRR</span></tt></a>).</p>
+(see module <a class="reference internal" href="TRR.html#module-MDAnalysis.coordinates.TRR" title="MDAnalysis.coordinates.TRR"><code class="xref py py-mod docutils literal"><span class="pre">TRR</span></code></a>).</p>
 <p>The XTC I/O interface uses
-<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt></a> to implement random
+<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code></a> to implement random
 access to frames. This works by initially building an internal index
 of all frames and then using this index for direct seeks. Building the
 index is triggered by
-<a class="reference internal" href="xdrfile/libxdrfile2.html#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_n_frames" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_n_frames"><tt class="xref py py-func docutils literal"><span class="pre">read_xtc_n_frames()</span></tt></a>,
+<a class="reference internal" href="xdrfile/libxdrfile2.html#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_n_frames" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_n_frames"><code class="xref py py-func docutils literal"><span class="pre">read_xtc_n_frames()</span></code></a>,
 which typically happens when one accesses the
-<a class="reference internal" href="#MDAnalysis.coordinates.XTC.XTCReader.n_frames" title="MDAnalysis.coordinates.XTC.XTCReader.n_frames"><tt class="xref py py-attr docutils literal"><span class="pre">XTCReader.n_frames</span></tt></a> attribute for the first time. Building the
+<a class="reference internal" href="#MDAnalysis.coordinates.XTC.XTCReader.n_frames" title="MDAnalysis.coordinates.XTC.XTCReader.n_frames"><code class="xref py py-attr docutils literal"><span class="pre">XTCReader.n_frames</span></code></a> attribute for the first time. Building the
 index may take many minutes for large trajectories but afterwards
 access is faster than with native Gromacs tools.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span>The XTC I/O interface now uses
-<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt></a>, which has
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span>The XTC I/O interface now uses
+<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code></a>, which has
 seeking and indexing capabilities. Note that unlike
-<tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></tt> before it,
-<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt></a> is distributed
+<code class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></code> before it,
+<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code></a> is distributed
 under the GNU GENERAL PUBLIC LICENSE, version 2 (or higher).
-<a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> now correctly
+<a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> now correctly
 deals with presence/absence of coordinate/velocity/force
 information on a per-frame basis.</p>
+</div>
 <div class="section" id="module-reference">
 <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.XTC.Timestep">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.XTC.</tt><tt class="descname">Timestep</tt><big>(</big><em>n_atoms</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.XTC.</code><code class="descname">Timestep</code><span class="sig-paren">(</span><em>n_atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/xdrfile/core.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Timestep for a Gromacs trajectory.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Attributes status, lmbda, prec all stored in the <tt class="xref py py-attr docutils literal"><span class="pre">data</span></tt> dictionary
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Attributes status, lmbda, prec all stored in the <code class="xref py py-attr docutils literal"><span class="pre">data</span></code> dictionary
 Native frame number now stored as <cite>_frame</cite>, was <cite>step</cite></p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.copy">
-<tt class="descname">copy</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.copy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>.</p>
+<code class="descname">copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.copy_slice">
-<tt class="descname">copy_slice</tt><big>(</big><em>sel</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
+<code class="descname">copy_slice</code><span class="sig-paren">(</span><em>sel</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy_slice"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
 <dd><p>Make a new Timestep containing a subset of the original Timestep.</p>
-<p><tt class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></tt>
-<tt class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></tt></p>
+<p><code class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></code>
+<code class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></code></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A Timestep object of the same type containing all header
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A Timestep object of the same type containing all header
 information and all atom information relevant to the selection.</td>
 </tr>
 </tbody>
@@ -166,16 +168,18 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 <p class="last">The selection must be a 0 based slice or array of the atom indices
 in this Timestep</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
 copy official attributes of the Timestep.</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.dimensions">
-<tt class="descname">dimensions</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>unitcell dimensions (A, B, C, alpha, beta, gamma)</p>
 <ul class="simple">
 <li>A, B, C are the lengths of the primitive cell vectors e1, e2, e3</li>
@@ -187,19 +191,20 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.dt" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dt</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.dt" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time difference in ps between timesteps</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">This defaults to 1.0 ps in the absence of time data</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.forces">
-<tt class="descname">forces</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.forces" title="Permalink to this definition">¶</a></dt>
+<code class="descname">forces</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.forces" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the forces of all atoms in this Timestep</p>
 <p>Setting this attribute will add forces to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -207,12 +212,12 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of force data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of force data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.NoDataError</span></tt></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.NoDataError</span></code></dt>
 <dd><p class="first last">When the Timestep does not contain force information</p>
 </dd>
 </dl>
@@ -220,67 +225,74 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
-<dl class="classmethod">
+<dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.from_coordinates">
-<em class="property">classmethod </em><tt class="descname">from_coordinates</tt><big>(</big><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
+<code class="descname">from_coordinates</code><span class="sig-paren">(</span><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_coordinates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create an instance of this Timestep, from coordinate data</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
-<dl class="classmethod">
+<dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.from_timestep">
-<em class="property">classmethod </em><tt class="descname">from_timestep</tt><big>(</big><em>other</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">from_timestep</code><span class="sig-paren">(</span><em>other</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a copy of another Timestep, in the format of this Timestep</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.has_forces">
-<tt class="descname">has_forces</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.has_forces" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_forces</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.has_forces" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has force data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.has_positions">
-<tt class="descname">has_positions</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.has_positions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_positions</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.has_positions" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has position data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.has_velocities">
-<tt class="descname">has_velocities</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.has_velocities" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_velocities</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.has_velocities" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has velocity data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.n_atoms">
-<tt class="descname">n_atoms</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>A read only view of the number of atoms this Timestep has</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.positions">
-<tt class="descname">positions</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.positions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">positions</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.positions" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the positions of all atoms in this Timestep</p>
 <p>Setting this attribute will add positions to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -288,12 +300,12 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of position data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of position data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></tt></a></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></code></a></dt>
 <dd><p class="first last">If the Timestep has no position data</p>
 </dd>
 </dl>
@@ -301,13 +313,14 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now can raise NoDataError when no position data present</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now can raise NoDataError when no position data present</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time in ps of this timestep</p>
 <p>This is calculated as:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">time</span>
@@ -317,19 +330,20 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span> <span class="o">*</span> <span class="n">ts</span><span class="o">.</span><span class="n">dt</span>
 </pre></div>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.triclinic_dimensions">
-<tt class="descname">triclinic_dimensions</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">triclinic_dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>The unitcell dimensions represented as triclinic vectors</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
 </tr>
 </tbody>
 </table>
@@ -349,17 +363,18 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 <span class="go">        72.45159912,  71.56504822], dtype=float32)</span>
 </pre></div>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.velocities">
-<tt class="descname">velocities</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.velocities" title="Permalink to this definition">¶</a></dt>
+<code class="descname">velocities</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.velocities" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the velocities of all atoms in this Timestep</p>
 <p>Setting this attribute will add velocities to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -367,12 +382,12 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of velocity data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of velocity data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></tt></a></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></code></a></dt>
 <dd><p class="first last">When the Timestep does not contain velocity information</p>
 </dd>
 </dl>
@@ -380,13 +395,14 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.Timestep.volume">
-<tt class="descname">volume</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.volume" title="Permalink to this definition">¶</a></dt>
+<code class="descname">volume</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.Timestep.volume" title="Permalink to this definition">¶</a></dt>
 <dd><p>volume of the unitcell</p>
 </dd></dl>
 
@@ -394,22 +410,23 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.XTC.</tt><tt class="descname">XTCReader</tt><big>(</big><em>filename</em>, <em>sub=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.XTC.</code><code class="descname">XTCReader</code><span class="sig-paren">(</span><em>filename</em>, <em>sub=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/xdrfile/XTC.html#XTCReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read <a class="reference external" href="http://www.gromacs.org">Gromacs</a> XTC trajectory.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Timestep attributes status and prec are now stored in the TS.data dictionary</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Timestep attributes status and prec are now stored in the TS.data dictionary</p>
+</div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">the name of the trr file.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>sub</em></dt>
 <dd><p class="first">an numpy integer array of what subset of trajectory atoms to load into
 the timestep. Intended to work similarly to the &#8216;sub&#8217; argument to <a class="reference external" href="http://www.gromacs.org">Gromacs</a>&#8216; trjconv.</p>
@@ -419,47 +436,50 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 equal to number of atoms in the Universe.</p>
 </dd>
 <dt><em>refresh_offsets</em></dt>
-<dd><p class="first last">if <tt class="docutils literal"><span class="pre">True</span></tt>, do not retrieve stored offsets, but instead generate
-new ones; if <tt class="docutils literal"><span class="pre">False</span></tt>, use retrieved offsets if available [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">if <code class="docutils literal"><span class="pre">True</span></code>, do not retrieve stored offsets, but instead generate
+new ones; if <code class="docutils literal"><span class="pre">False</span></code>, use retrieved offsets if available [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>refresh_offsets</em></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Renamed &#8220;delta&#8221; attribute to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>refresh_offsets</em></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Renamed &#8220;delta&#8221; attribute to &#8220;dt&#8221;
+Now passes weakref of self to ts (as &#8220;_reader&#8221;)</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.OtherWriter">
-<tt class="descname">OtherWriter</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">OtherWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a writer appropriate for <em>filename</em>.</p>
 <p>Sets the default keywords <em>start</em>, <em>step</em> and <em>dt</em> (if
-available). <em>n_atoms</em> is always set from <tt class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></tt>.</p>
-<div class="admonition-see-also admonition seealso">
+available). <em>n_atoms</em> is always set from <code class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></code>.</p>
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></tt> and <tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></tt></p>
+<p class="last"><code class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></code> and <code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a Gromacs TrjWriter for <em>filename</em> with the same parameters as this trajectory.</p>
 <p>All values can be changed through keyword arguments.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">number of atoms</p>
 </dd>
@@ -473,132 +493,139 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">appropriate <tt class="xref py py-class docutils literal"><span class="pre">TrjWriter</span></tt></p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">appropriate <code class="xref py py-class docutils literal"><span class="pre">TrjWriter</span></code></p>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Changed &#8220;delta&#8221; keyword to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Changed &#8220;delta&#8221; keyword to &#8220;dt&#8221;</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close xdr trajectory file if it was open.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.dt" title="Permalink to this definition">¶</a></dt>
-<dd><p>Time step length in ps.</p>
-<p>The result is computed from the trajectory and cached. If for
-any reason the trajectory cannot be read then 0 is returned.</p>
+<code class="descname">dt</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.dt" title="Permalink to this definition">¶</a></dt>
+<dd><p>Time between two trajectory frames in picoseconds.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.frame">
-<tt class="descname">frame</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.frame" title="Permalink to this definition">¶</a></dt>
+<code class="descname">frame</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.frame" title="Permalink to this definition">¶</a></dt>
 <dd><p>Frame number of the current time step.</p>
-<p>This is a simple short cut to <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt>.</p>
+<p>This is a simple short cut to <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.load_offsets">
-<tt class="descname">load_offsets</tt><big>(</big><em>filename</em>, <em>check=False</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.load_offsets" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_offsets</code><span class="sig-paren">(</span><em>filename</em>, <em>check=False</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.load_offsets" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads current trajectory offsets from pickled <em>filename</em>.</p>
 <p>Checks if ctime and size of trajectory file matches that stored in
-pickled <em>filename</em>.  If either one does not match (and <em>check</em> == <tt class="docutils literal"><span class="pre">True</span></tt>)
+pickled <em>filename</em>.  If either one does not match (and <em>check</em> == <code class="docutils literal"><span class="pre">True</span></code>)
 then the offsets are not loaded.  This is intended to conservatively
 avoid loading out-of-date offsets.</p>
 <dl class="docutils">
@@ -617,22 +644,22 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
-<dd><p class="first last">filename of pickle file saved with <tt class="xref py py-meth docutils literal"><span class="pre">save_offsets()</span></tt> 
+<dd><p class="first last">filename of pickle file saved with <code class="xref py py-meth docutils literal"><span class="pre">save_offsets()</span></code> 
 with the frame offsets for the loaded trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>check</em></dt>
 <dd><p class="first last">if False, ignore ctime and size check of trajectory file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> if the file cannot be read (see <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">open()</span></tt></a>).</p>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> if the file cannot be read (see <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">open()</span></code></a>).</p>
 </td>
 </tr>
 </tbody>
@@ -641,7 +668,7 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.n_atoms">
-<tt class="descname">n_atoms</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>The number of publically available atoms that this reader will store in the timestep.</p>
 <p>If &#8216;sub&#8217; was not given in the ctor, then this value will just be the actual
 number of atoms in the underlying trajectory file. If however &#8216;sub&#8217; was given, then
@@ -651,7 +678,7 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.n_frames">
-<tt class="descname">n_frames</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.n_frames" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_frames</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.n_frames" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the number of frames from the trajectory.</p>
 <p>The result is cached. If for any reason the trajectory cannot
 be read then 0 is returned.</p>
@@ -659,29 +686,29 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 iterating through the whole trajectory. If the trajectory
 was previously loaded and saved offsets exist, then
 loading will be significantly faster.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-meth docutils literal"><span class="pre">TrjReader.load_offsets()</span></tt> and <tt class="xref py py-meth docutils literal"><span class="pre">TrjReader.save_offsets()</span></tt></p>
+<p class="last"><code class="xref py py-meth docutils literal"><span class="pre">TrjReader.load_offsets()</span></code> and <code class="xref py py-meth docutils literal"><span class="pre">TrjReader.save_offsets()</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.next">
-<tt class="descname">next</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.next" title="Permalink to this definition">¶</a></dt>
+<code class="descname">next</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.next" title="Permalink to this definition">¶</a></dt>
 <dd><p>Forward one step to next frame.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.open_trajectory">
-<tt class="descname">open_trajectory</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
+<code class="descname">open_trajectory</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
 <dd><p>Open xdr trajectory file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">pointer to XDRFILE (and sets self.xdrfile)</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">pointer to XDRFILE (and sets self.xdrfile)</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> with code EALREADY if file was already opened or
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> with code EALREADY if file was already opened or
 ENOENT if the file cannot be found</td>
 </tr>
 </tbody>
@@ -690,13 +717,13 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.rewind">
-<tt class="descname">rewind</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.rewind" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rewind</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.rewind" title="Permalink to this definition">¶</a></dt>
 <dd><p>Position at beginning of trajectory</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.save_offsets">
-<tt class="descname">save_offsets</tt><big>(</big><em>filename</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.save_offsets" title="Permalink to this definition">¶</a></dt>
+<code class="descname">save_offsets</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.save_offsets" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves current trajectory offsets into <em>filename</em>, as a pickled object.</p>
 <p>Along with the offsets themselves, the ctime and file size of the
 trajectory file are also saved.  These are used upon load as a check to
@@ -718,7 +745,7 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename in which to save the frame offsets</p>
 </dd>
@@ -731,15 +758,15 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>Time of the current frame in MDAnalysis time units (typically ps).</p>
 <p>This is either read straight from the Timestep, or calculated as
-time = <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt> * <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep.dt" title="MDAnalysis.coordinates.XTC.Timestep.dt"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></tt></a></p>
+time = <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code> * <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep.dt" title="MDAnalysis.coordinates.XTC.Timestep.dt"><code class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></code></a></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XTC.XTCReader.totaltime">
-<tt class="descname">totaltime</tt><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.totaltime" title="Permalink to this definition">¶</a></dt>
+<code class="descname">totaltime</code><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCReader.totaltime" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total length of the trajectory n_frames * dt.</p>
 </dd></dl>
 
@@ -747,14 +774,14 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.XTC.</tt><tt class="descname">XTCWriter</tt><big>(</big><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=None</em>, <em>precision=1000.0</em>, <em>remarks=None</em>, <em>convert_units=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.XTC.</code><code class="descname">XTCWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=None</em>, <em>precision=1000.0</em>, <em>remarks=None</em>, <em>convert_units=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/xdrfile/XTC.html#XTCWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a <a class="reference external" href="http://www.gromacs.org">Gromacs</a> XTC trajectory.</p>
 <p>Create a new TrjWriter</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of output file</p>
 </dd>
@@ -764,7 +791,7 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>start</em></dt>
 <dd><p class="first last">starting timestep frame; only used when <em>dt</em> is set.</p>
 </dd>
@@ -773,9 +800,9 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 </dd>
 <dt><em>dt</em></dt>
 <dd><p class="first last">time between frames to use. If set will override any time information
-contained in the passed <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects, which will otherwise
+contained in the passed <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects, which will otherwise
 be used.
-The <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep.time" title="MDAnalysis.coordinates.XTC.Timestep.time"><tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt></a> attribute defaults to a timestep of
+The <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep.time" title="MDAnalysis.coordinates.XTC.Timestep.time"><code class="xref py py-attr docutils literal"><span class="pre">time</span></code></a> attribute defaults to a timestep of
 to setting the trajectory time at 1 ps per step if there is no
 time information.</p>
 </dd>
@@ -784,121 +811,131 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 for TRR) [1000.0]</p>
 </dd>
 <dt><em>convert_units</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: units are converted to the MDAnalysis base format; <tt class="docutils literal"><span class="pre">None</span></tt> selects
-the value of <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> [&#8216;convert_lengths&#8217;].
-(see <a class="reference internal" href="../core/init.html#flags-label"><em>Flags</em></a>)</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: units are converted to the MDAnalysis base format; <code class="docutils literal"><span class="pre">None</span></code> selects
+the value of <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> [&#8216;convert_lengths&#8217;].
+(see <a class="reference internal" href="../core/init.html#flags-label"><span>Flags</span></a>)</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span>The TRR writer is now able to write TRRs without coordinates/velocities/forces,
-depending on the properties available in the <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects passed to
-<tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Keyword &#8220;delta&#8221; renamed to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span>The TRR writer is now able to write TRRs without coordinates/velocities/forces,
+depending on the properties available in the <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects passed to
+<code class="xref py py-meth docutils literal"><span class="pre">write()</span></code>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Keyword &#8220;delta&#8221; renamed to &#8220;dt&#8221;</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.convert_dimensions_to_unitcell">
-<tt class="descname">convert_dimensions_to_unitcell</tt><big>(</big><em>ts</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_dimensions_to_unitcell</code><span class="sig-paren">(</span><em>ts</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read dimensions from timestep <em>ts</em> and return Gromacs box vectors</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.has_valid_coordinates">
-<tt class="descname">has_valid_coordinates</tt><big>(</big><em>criteria</em>, <em>x</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns <tt class="docutils literal"><span class="pre">True</span></tt> if all values are within limit values of their formats.</p>
+<code class="descname">has_valid_coordinates</code><span class="sig-paren">(</span><em>criteria</em>, <em>x</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns <code class="docutils literal"><span class="pre">True</span></code> if all values are within limit values of their formats.</p>
 <p>Due to rounding, the test is asymmetric (and <em>min</em> is supposed to be negative):</p>
 <blockquote>
 <div>min &lt; x &lt;= max</div></blockquote>
@@ -906,17 +943,17 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>criteria</em></dt>
 <dd><p class="first last">dictionary containing the <em>max</em> and <em>min</em> values in native units</p>
 </dd>
 <dt><em>x</em></dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></tt> of <tt class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></tt> coordinates of atoms selected to be written out.</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></code> of <code class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></code> coordinates of atoms selected to be written out.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">boolean</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">boolean</p>
 </td>
 </tr>
 </tbody>
@@ -925,10 +962,10 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.write">
-<tt class="descname">write</tt><big>(</big><em>obj</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write current timestep, using the supplied <em>obj</em>.</p>
-<p>The argument should be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> or
-a <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> or a <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance.</p>
+<p>The argument should be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> or
+a <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> or a <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The size of the <em>obj</em> must be the same as the number of atom
@@ -938,9 +975,9 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XTC.XTCWriter.write_next_timestep">
-<tt class="descname">write_next_timestep</tt><big>(</big><em>ts=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_next_timestep</code><span class="sig-paren">(</span><em>ts=None</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.XTC.XTCWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>write a new timestep to the trj file</p>
-<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance containing coordinates to
+<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.XTC.Timestep" title="MDAnalysis.coordinates.XTC.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance containing coordinates to
 be written to trajectory file</p>
 </dd></dl>
 
@@ -955,7 +992,7 @@ <h2>5.16.1. Module reference<a class="headerlink" href="#module-reference" title
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -970,11 +1007,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="TRR.html" title="5.15. Gromacs TRR file IO — MDAnalysis.coordinates.TRR"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -984,7 +1021,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/XYZ.html b/package/doc/html/documentation_pages/coordinates/XYZ.html
index 32ee28bc37a..9dd563e1014 100644
--- a/package/doc/html/documentation_pages/coordinates/XYZ.html
+++ b/package/doc/html/documentation_pages/coordinates/XYZ.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.17. XYZ trajectory reader — MDAnalysis.coordinates.XYZ &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.17. XYZ trajectory reader — MDAnalysis.coordinates.XYZ &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.18. TRZ trajectory I/O — MDAnalysis.coordinates.TRZ" href="TRZ.html" />
     <link rel="prev" title="5.16. Gromacs XTC file IO — MDAnalysis.coordinates.XTC" href="XTC.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="XTC.html" title="5.16. Gromacs XTC file IO — MDAnalysis.coordinates.XTC"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.17. XYZ trajectory reader &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.XYZ</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.17. XYZ trajectory reader &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.XYZ</span></code></a><ul>
 <li><a class="reference internal" href="#xyz-file-format">5.17.1. XYZ File format</a></li>
 </ul>
 </li>
@@ -70,16 +68,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="XTC.html"
-                        title="previous chapter">5.16. Gromacs XTC file IO &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></tt></a></p>
+                        title="previous chapter">5.16. Gromacs XTC file IO &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="TRZ.html"
-                        title="next chapter">5.18. TRZ trajectory I/O  &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.TRZ</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/XYZ.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.18. TRZ trajectory I/O  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRZ</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/XYZ.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,11 +98,11 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.XYZ"></span><div class="section" id="xyz-trajectory-reader-mdanalysis-coordinates-xyz">
-<h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.XYZ" title="MDAnalysis.coordinates.XYZ"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.XYZ</span></tt></a><a class="headerlink" href="#xyz-trajectory-reader-mdanalysis-coordinates-xyz" title="Permalink to this headline">¶</a></h1>
-<p>The <a class="reference internal" href="#xyz-format"><em>XYZ format</em></a> is a loosely defined, simple
+<h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.XYZ" title="MDAnalysis.coordinates.XYZ"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.XYZ</span></code></a><a class="headerlink" href="#xyz-trajectory-reader-mdanalysis-coordinates-xyz" title="Permalink to this headline">¶</a></h1>
+<p>The <a class="reference internal" href="#xyz-format"><span>XYZ format</span></a> is a loosely defined, simple
 coordinate trajectory format. The implemented format definition was
 taken from the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html">VMD xyzplugin</a> and is therefore compatible with VMD.</p>
 <p>Note the following:</p>
@@ -126,15 +126,16 @@ <h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#mod
 will need to tweak this class.</p>
 <div class="section" id="xyz-file-format">
 <span id="xyz-format"></span><h2>5.17.1. XYZ File format<a class="headerlink" href="#xyz-file-format" title="Permalink to this headline">¶</a></h2>
-<p>Definiton used by the <a class="reference internal" href="#MDAnalysis.coordinates.XYZ.XYZReader" title="MDAnalysis.coordinates.XYZ.XYZReader"><tt class="xref py py-class docutils literal"><span class="pre">XYZReader</span></tt></a> and <a class="reference internal" href="#MDAnalysis.coordinates.XYZ.XYZWriter" title="MDAnalysis.coordinates.XYZ.XYZWriter"><tt class="xref py py-class docutils literal"><span class="pre">XYZWriter</span></tt></a> (and
+<p>Definiton used by the <a class="reference internal" href="#MDAnalysis.coordinates.XYZ.XYZReader" title="MDAnalysis.coordinates.XYZ.XYZReader"><code class="xref py py-class docutils literal"><span class="pre">XYZReader</span></code></a> and <a class="reference internal" href="#MDAnalysis.coordinates.XYZ.XYZWriter" title="MDAnalysis.coordinates.XYZ.XYZWriter"><code class="xref py py-class docutils literal"><span class="pre">XYZWriter</span></code></a> (and
 the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html">VMD xyzplugin</a> from whence the definition was taken):</p>
-<div class="highlight-python"><pre>[ comment line            ] !! NOT IMPLEMENTED !! DO NOT INCLUDE
+<div class="highlight-python"><div class="highlight"><pre>[ comment line            ] !! NOT IMPLEMENTED !! DO NOT INCLUDE
 [ N                       ] # of atoms, required by this xyz reader plugin  line 1
 [ molecule name           ] name of molecule (can be blank)                 line 2
 atom1 x y z [optional data] atom name followed by xyz coords                line 3
 atom2 x y z [ ...         ] and (optionally) other data.
 ...
-atomN x y z [ ...         ]                                                 line N+2</pre>
+atomN x y z [ ...         ]                                                 line N+2
+</pre></div>
 </div>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
@@ -147,24 +148,24 @@ <h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#mod
 </div>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.XYZ.XYZReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.XYZ.</tt><tt class="descname">XYZReader</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.XYZ.</code><code class="descname">XYZReader</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reads from an XYZ file</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Data :</th><td class="field-body"><dl class="first docutils">
-<dt><tt class="xref py py-attr docutils literal"><span class="pre">ts</span></tt></dt>
+<tr class="field-odd field"><th class="field-name">Data:</th><td class="field-body"><dl class="first docutils">
+<dt><code class="xref py py-attr docutils literal"><span class="pre">ts</span></code></dt>
 <dd><p class="first last">Timestep object containing coordinates of current frame</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Methods :</th><td class="field-body"><dl class="first last docutils">
-<dt><tt class="docutils literal"><span class="pre">len(xyz)</span></tt></dt>
+<tr class="field-even field"><th class="field-name">Methods:</th><td class="field-body"><dl class="first last docutils">
+<dt><code class="docutils literal"><span class="pre">len(xyz)</span></code></dt>
 <dd><p class="first last">return number of frames in xyz</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">xyz:</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">for</span> <span class="pre">ts</span> <span class="pre">in</span> <span class="pre">xyz:</span></code></dt>
 <dd><p class="first last">iterate through trajectory</p>
 </dd>
 </dl>
@@ -173,34 +174,35 @@ <h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#mod
 </tbody>
 </table>
 <p>The XYZ file format follows VMD&#8217;s <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html">xyzplugin</a> and is also described
-under <a class="reference internal" href="#xyz-format"><em>XYZ format</em></a>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based. Added <em>dt</em> and
-<em>time_offset</em> keywords (passed to <tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt>)</p>
+under <a class="reference internal" href="#xyz-format"><span>XYZ format</span></a>.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based. Added <em>dt</em> and
+<em>time_offset</em> keywords (passed to <code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code>)</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XYZ.XYZReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a XYZWriter for <em>filename</em> with the same parameters as this XYZ.</p>
 <p>All values can be changed through keyword arguments.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output DCD trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>atoms</em></dt>
 <dd><p class="first last">names of the atoms (if not taken from atom groups)</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.XYZ.XYZWriter" title="MDAnalysis.coordinates.XYZ.XYZWriter"><tt class="xref py py-class docutils literal"><span class="pre">XYZWriter</span></tt></a> (see there for more details)</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.XYZ.XYZWriter" title="MDAnalysis.coordinates.XYZ.XYZWriter"><code class="xref py py-class docutils literal"><span class="pre">XYZWriter</span></code></a> (see there for more details)</p>
 </td>
 </tr>
 </tbody>
@@ -209,19 +211,19 @@ <h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#mod
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XYZ.XYZReader.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZReader.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZReader.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZReader.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZReader.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close xyz trajectory file if it was open.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.XYZ.XYZReader.n_atoms">
-<tt class="descname">n_atoms</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZReader.n_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZReader.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZReader.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>number of atoms in a frame</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XYZ.XYZReader.rewind">
-<tt class="descname">rewind</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZReader.rewind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZReader.rewind" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rewind</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZReader.rewind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZReader.rewind" title="Permalink to this definition">¶</a></dt>
 <dd><p>reposition on first frame</p>
 </dd></dl>
 
@@ -229,7 +231,7 @@ <h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#mod
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.XYZ.XYZWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.XYZ.</tt><tt class="descname">XYZWriter</tt><big>(</big><em>*args</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.XYZ.</code><code class="descname">XYZWriter</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Writes an XYZ file</p>
 <p>The XYZ file format is not formally defined. This writer follows
 the VMD implementation for the molfile <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html">xyzplugin</a>.</p>
@@ -238,7 +240,7 @@ <h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#mod
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">file name of trajectory file. If it ends with &#8220;gz&#8221; then the file
 will be gzip-compressed; if it ends with &#8220;bz2&#8221; it will be bzip2
@@ -247,16 +249,16 @@ <h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#mod
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>atoms</em></dt>
 <dd><p class="first">Provide atom names: This can be a list of names or an
-<tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt>.  If none is provided, atoms will
+<code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code>.  If none is provided, atoms will
 be called &#8216;X&#8217; in the output. These atom names will be
 used when a trajectory is written from raw
-<tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt> objects which do not contain atom
+<code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code> objects which do not contain atom
 information.</p>
-<p class="last">If you write a <tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt> with
-<a class="reference internal" href="#MDAnalysis.coordinates.XYZ.XYZWriter.write" title="MDAnalysis.coordinates.XYZ.XYZWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">XYZWriter.write()</span></tt></a> then atom information is taken
+<p class="last">If you write a <code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code> with
+<a class="reference internal" href="#MDAnalysis.coordinates.XYZ.XYZWriter.write" title="MDAnalysis.coordinates.XYZ.XYZWriter.write"><code class="xref py py-meth docutils literal"><span class="pre">XYZWriter.write()</span></code></a> then atom information is taken
 at each step and <em>atoms</em> is ignored.</p>
 </dd>
 <dt><em>remark</em></dt>
@@ -269,27 +271,27 @@ <h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#mod
 </table>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XYZ.XYZWriter.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZWriter.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZWriter.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZWriter.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZWriter.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file and finalize the writing</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XYZ.XYZWriter.write">
-<tt class="descname">write</tt><big>(</big><em>obj</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write object <em>obj</em> at current trajectory frame to file.</p>
-<p><em>obj</em> can be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>)
-or a whole <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>.</p>
+<p><em>obj</em> can be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>)
+or a whole <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>.</p>
 <p>Atom names in the output are taken from the <em>obj</em> or default
 to the value of the <em>atoms</em> keyword supplied to the
-<a class="reference internal" href="#MDAnalysis.coordinates.XYZ.XYZWriter" title="MDAnalysis.coordinates.XYZ.XYZWriter"><tt class="xref py py-class docutils literal"><span class="pre">XYZWriter</span></tt></a> constructor.</p>
+<a class="reference internal" href="#MDAnalysis.coordinates.XYZ.XYZWriter" title="MDAnalysis.coordinates.XYZ.XYZWriter"><code class="xref py py-class docutils literal"><span class="pre">XYZWriter</span></code></a> constructor.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>obj</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> or
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a></p>
+<dd><p class="first last"><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> or
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a></p>
 </dd>
 </dl>
 </td>
@@ -300,7 +302,7 @@ <h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#mod
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.XYZ.XYZWriter.write_next_timestep">
-<tt class="descname">write_next_timestep</tt><big>(</big><em>ts=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZWriter.write_next_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_next_timestep</code><span class="sig-paren">(</span><em>ts=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/XYZ.html#XYZWriter.write_next_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.XYZ.XYZWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write coordinate information in <em>ts</em> to the trajectory</p>
 </dd></dl>
 
@@ -315,7 +317,7 @@ <h1>5.17. XYZ trajectory reader &#8212; <a class="reference internal" href="#mod
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -330,11 +332,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="XTC.html" title="5.16. Gromacs XTC file IO — MDAnalysis.coordinates.XTC"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -344,7 +346,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/base.html b/package/doc/html/documentation_pages/coordinates/base.html
index 407d9814ccc..5c42690708c 100644
--- a/package/doc/html/documentation_pages/coordinates/base.html
+++ b/package/doc/html/documentation_pages/coordinates/base.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.19. Base classes — MDAnalysis.coordinates.base &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.19. Base classes — MDAnalysis.coordinates.base &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.20. Common functions for coordinate reading — MDAnalysis.coordinates.core" href="core.html" />
     <link rel="prev" title="5.18. TRZ trajectory I/O — MDAnalysis.coordinates.TRZ" href="TRZ.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="TRZ.html" title="5.18. TRZ trajectory I/O — MDAnalysis.coordinates.TRZ"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="TRZ.html"
-                        title="previous chapter">5.18. TRZ trajectory I/O  &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.TRZ</span></tt></a></p>
+                        title="previous chapter">5.18. TRZ trajectory I/O  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRZ</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="core.html"
-                        title="next chapter">5.20. Common functions for coordinate reading &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.core</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/base.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.20. Common functions for coordinate reading &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.core</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/base.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,43 +90,43 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.base"></span><div class="section" id="base-classes-mdanalysis-coordinates-base">
-<h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.base" title="MDAnalysis.coordinates.base"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></tt></a><a class="headerlink" href="#base-classes-mdanalysis-coordinates-base" title="Permalink to this headline">¶</a></h1>
+<h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.base" title="MDAnalysis.coordinates.base"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></code></a><a class="headerlink" href="#base-classes-mdanalysis-coordinates-base" title="Permalink to this headline">¶</a></h1>
 <p>Derive other Timestep, Reader and Writer classes from the classes in this
 module. The derived classes must follow the Trajectory API in
-<a class="reference internal" href="init.html#module-MDAnalysis.coordinates.__init__" title="MDAnalysis.coordinates.__init__"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.__init__</span></tt></a>.</p>
+<a class="reference internal" href="init.html#module-MDAnalysis.coordinates.__init__" title="MDAnalysis.coordinates.__init__"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.__init__</span></code></a>.</p>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.base.Timestep">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.base.</tt><tt class="descname">Timestep</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.base.</code><code class="descname">Timestep</code><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep" title="Permalink to this definition">¶</a></dt>
 <dd><dl class="method">
 <dt id="MDAnalysis.coordinates.base.Timestep.__init__">
-<tt class="descname">__init__</tt><big>(</big><em>n_atoms</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.__init__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.__init__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__init__</code><span class="sig-paren">(</span><em>n_atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.__init__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.__init__" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a Timestep, representing a frame of a trajectory</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">The total number of atoms this Timestep describes</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>positions</em></dt>
-<dd><p class="first last">Whether this Timestep has position information [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has position information [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 <dt><em>velocities</em></dt>
-<dd><p class="first last">Whether this Timestep has velocity information [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has velocity information [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>forces</em></dt>
-<dd><p class="first last">Whether this Timestep has force information [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">Whether this Timestep has force information [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>dt</em></dt>
-<dd><p class="first last">The time difference between frames (ps).  If <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep.time" title="MDAnalysis.coordinates.base.Timestep.time"><tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt></a>
+<dd><p class="first last">The time difference between frames (ps).  If <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep.time" title="MDAnalysis.coordinates.base.Timestep.time"><code class="xref py py-attr docutils literal"><span class="pre">time</span></code></a>
 is set, then <cite>dt</cite> will be ignored.</p>
 </dd>
 <dt><em>time_offset</em></dt>
@@ -137,45 +137,49 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Added keywords for positions, velocities and forces
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Added keywords for positions, velocities and forces
 Can add and remove position/velocity/force information by using
 the has_* attribute</p>
+</div>
 </dd></dl>
 
 <dl class="classmethod">
 <dt id="MDAnalysis.coordinates.base.Timestep.from_coordinates">
-<em class="property">classmethod </em><tt class="descname">from_coordinates</tt><big>(</big><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_coordinates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
+<em class="property">classmethod </em><code class="descname">from_coordinates</code><span class="sig-paren">(</span><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_coordinates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create an instance of this Timestep, from coordinate data</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="classmethod">
 <dt id="MDAnalysis.coordinates.base.Timestep.from_timestep">
-<em class="property">classmethod </em><tt class="descname">from_timestep</tt><big>(</big><em>other</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
+<em class="property">classmethod </em><code class="descname">from_timestep</code><span class="sig-paren">(</span><em>other</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a copy of another Timestep, in the format of this Timestep</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.Timestep._init_unitcell">
-<tt class="descname">_init_unitcell</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep._init_unitcell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep._init_unitcell" title="Permalink to this definition">¶</a></dt>
-<dd><p>Create custom datastructure for <tt class="xref py py-attr docutils literal"><span class="pre">_unitcell</span></tt>.</p>
+<code class="descname">_init_unitcell</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep._init_unitcell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep._init_unitcell" title="Permalink to this definition">¶</a></dt>
+<dd><p>Create custom datastructure for <code class="xref py py-attr docutils literal"><span class="pre">_unitcell</span></code>.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.n_atoms">
-<tt class="descname">n_atoms</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.n_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>A read only view of the number of atoms this Timestep has</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.time">
-<tt class="descname">time</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.time"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time in ps of this timestep</p>
 <p>This is calculated as:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">time</span>
@@ -185,25 +189,27 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span> <span class="o">*</span> <span class="n">ts</span><span class="o">.</span><span class="n">dt</span>
 </pre></div>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.dt">
-<tt class="descname">dt</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.dt"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.dt" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dt</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.dt" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time difference in ps between timesteps</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">This defaults to 1.0 ps in the absence of time data</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.positions">
-<tt class="descname">positions</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.positions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.positions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">positions</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.positions" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the positions of all atoms in this Timestep</p>
 <p>Setting this attribute will add positions to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -211,12 +217,12 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of position data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of position data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></tt></a></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></code></a></dt>
 <dd><p class="first last">If the Timestep has no position data</p>
 </dd>
 </dl>
@@ -224,13 +230,14 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now can raise NoDataError when no position data present</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now can raise NoDataError when no position data present</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.velocities">
-<tt class="descname">velocities</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.velocities"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.velocities" title="Permalink to this definition">¶</a></dt>
+<code class="descname">velocities</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.velocities" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the velocities of all atoms in this Timestep</p>
 <p>Setting this attribute will add velocities to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -238,12 +245,12 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of velocity data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of velocity data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></tt></a></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></code></a></dt>
 <dd><p class="first last">When the Timestep does not contain velocity information</p>
 </dd>
 </dl>
@@ -251,13 +258,14 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.forces">
-<tt class="descname">forces</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.forces"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.forces" title="Permalink to this definition">¶</a></dt>
+<code class="descname">forces</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.forces" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the forces of all atoms in this Timestep</p>
 <p>Setting this attribute will add forces to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -265,12 +273,12 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of force data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of force data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.NoDataError</span></tt></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.NoDataError</span></code></dt>
 <dd><p class="first last">When the Timestep does not contain force information</p>
 </dd>
 </dl>
@@ -278,93 +286,99 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.has_positions">
-<tt class="descname">has_positions</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.has_positions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.has_positions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_positions</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.has_positions" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has position data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.has_velocities">
-<tt class="descname">has_velocities</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.has_velocities"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.has_velocities" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_velocities</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.has_velocities" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has velocity data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.has_forces">
-<tt class="descname">has_forces</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.has_forces"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.has_forces" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_forces</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.has_forces" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has force data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep._pos">
-<tt class="descname">_pos</tt><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep._pos" title="Permalink to this definition">¶</a></dt>
-<dd><p><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> of dtype <tt class="xref py py-class docutils literal"><span class="pre">float32</span></tt> of shape
+<code class="descname">_pos</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep._pos" title="Permalink to this definition">¶</a></dt>
+<dd><p><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> of dtype <code class="xref py py-class docutils literal"><span class="pre">float32</span></code> of shape
 (<em>n_atoms</em>, 3) and internal FORTRAN order, holding the raw
 cartesian coordinates (in MDAnalysis units, i.e. Å).</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">Normally one does not directly access <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep._pos" title="MDAnalysis.coordinates.base.Timestep._pos"><tt class="xref py py-attr docutils literal"><span class="pre">_pos</span></tt></a> but uses
-the <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><tt class="xref py py-meth docutils literal"><span class="pre">coordinates()</span></tt></a>
-method of an <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> but
+<p class="last">Normally one does not directly access <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep._pos" title="MDAnalysis.coordinates.base.Timestep._pos"><code class="xref py py-attr docutils literal"><span class="pre">_pos</span></code></a> but uses
+the <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><code class="xref py py-meth docutils literal"><span class="pre">coordinates()</span></code></a>
+method of an <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> but
 sometimes it can be faster to directly use the raw
 coordinates. Any changes to this array are immediately
 reflected in atom positions. If the frame is written to a new
 trajectory then the coordinates are changed. If a new
 trajectory frame is loaded, then <em>all</em> contents of
-<a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep._pos" title="MDAnalysis.coordinates.base.Timestep._pos"><tt class="xref py py-attr docutils literal"><span class="pre">_pos</span></tt></a> are overwritten.</p>
+<a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep._pos" title="MDAnalysis.coordinates.base.Timestep._pos"><code class="xref py py-attr docutils literal"><span class="pre">_pos</span></code></a> are overwritten.</p>
 </div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep._velocities">
-<tt class="descname">_velocities</tt><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep._velocities" title="Permalink to this definition">¶</a></dt>
-<dd><p><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> of dtype <tt class="xref py py-class docutils literal"><span class="pre">float32</span></tt>. of shape
+<code class="descname">_velocities</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep._velocities" title="Permalink to this definition">¶</a></dt>
+<dd><p><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> of dtype <code class="xref py py-class docutils literal"><span class="pre">float32</span></code>. of shape
 (<em>n_atoms</em>, 3), holding the raw velocities (in MDAnalysis
 units, i.e. typically Å/ps).</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p>Normally velocities are accessed through the
-<a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep.velocities" title="MDAnalysis.coordinates.base.Timestep.velocities"><tt class="xref py py-attr docutils literal"><span class="pre">velocities</span></tt></a> or the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.velocities"><tt class="xref py py-meth docutils literal"><span class="pre">velocities()</span></tt></a>
-method of an <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep._velocities" title="MDAnalysis.coordinates.base.Timestep._velocities"><tt class="xref py py-attr docutils literal"><span class="pre">_velocities</span></tt></a> only exists if the <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep.has_velocities" title="MDAnalysis.coordinates.base.Timestep.has_velocities"><tt class="xref py py-attr docutils literal"><span class="pre">has_velocities</span></tt></a>
+<a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep.velocities" title="MDAnalysis.coordinates.base.Timestep.velocities"><code class="xref py py-attr docutils literal"><span class="pre">velocities</span></code></a> or the
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.velocities"><code class="xref py py-meth docutils literal"><span class="pre">velocities()</span></code></a>
+method of an <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep._velocities" title="MDAnalysis.coordinates.base.Timestep._velocities"><code class="xref py py-attr docutils literal"><span class="pre">_velocities</span></code></a> only exists if the <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep.has_velocities" title="MDAnalysis.coordinates.base.Timestep.has_velocities"><code class="xref py py-attr docutils literal"><span class="pre">has_velocities</span></code></a>
 flag is True</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep._forces">
-<tt class="descname">_forces</tt><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep._forces" title="Permalink to this definition">¶</a></dt>
-<dd><p><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> of dtype <tt class="xref py py-class docutils literal"><span class="pre">float32</span></tt>. of shape
+<code class="descname">_forces</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep._forces" title="Permalink to this definition">¶</a></dt>
+<dd><p><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> of dtype <code class="xref py py-class docutils literal"><span class="pre">float32</span></code>. of shape
 (<em>n_atoms</em>, 3), holding the forces</p>
-<p><a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep._forces" title="MDAnalysis.coordinates.base.Timestep._forces"><tt class="xref py py-attr docutils literal"><span class="pre">_forces</span></tt></a> only exists if <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep.has_forces" title="MDAnalysis.coordinates.base.Timestep.has_forces"><tt class="xref py py-attr docutils literal"><span class="pre">has_forces</span></tt></a>
+<p><a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep._forces" title="MDAnalysis.coordinates.base.Timestep._forces"><code class="xref py py-attr docutils literal"><span class="pre">_forces</span></code></a> only exists if <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep.has_forces" title="MDAnalysis.coordinates.base.Timestep.has_forces"><code class="xref py py-attr docutils literal"><span class="pre">has_forces</span></code></a>
 is True</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0: </span>Added as optional to <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0: </span>Added as optional to <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.dimensions">
-<tt class="descname">dimensions</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.dimensions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>unitcell dimensions (<em>A</em>, <em>B</em>, <em>C</em>, <em>alpha</em>, <em>beta</em>, <em>gamma</em>)</p>
 <p>lengths <em>a</em>, <em>b</em>, <em>c</em> are in the MDAnalysis length unit (Å), and
 angles are in degrees.</p>
@@ -374,13 +388,13 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.triclinic_dimensions">
-<tt class="descname">triclinic_dimensions</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.triclinic_dimensions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">triclinic_dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>The unitcell dimensions represented as triclinic vectors</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
 </tr>
 </tbody>
 </table>
@@ -400,68 +414,70 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 <span class="go">        72.45159912,  71.56504822], dtype=float32)</span>
 </pre></div>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.Timestep.volume">
-<tt class="descname">volume</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.volume"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.volume" title="Permalink to this definition">¶</a></dt>
+<code class="descname">volume</code><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.volume" title="Permalink to this definition">¶</a></dt>
 <dd><p>volume of the unitcell</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.Timestep.__getitem__">
-<tt class="descname">__getitem__</tt><big>(</big><em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.__getitem__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.__getitem__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.__getitem__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.__getitem__" title="Permalink to this definition">¶</a></dt>
 <dd><p>Get a selection of coordinates</p>
-<p><tt class="docutils literal"><span class="pre">ts[i]</span></tt></p>
+<p><code class="docutils literal"><span class="pre">ts[i]</span></code></p>
 <blockquote>
 <div>return coordinates for the i&#8217;th atom (0-based)</div></blockquote>
-<p><tt class="docutils literal"><span class="pre">ts[start:stop:skip]</span></tt></p>
+<p><code class="docutils literal"><span class="pre">ts[start:stop:skip]</span></code></p>
 <blockquote>
 <div>return an array of coordinates, where start, stop and skip
 correspond to atom indices,
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.index" title="MDAnalysis.core.AtomGroup.Atom.index"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.index</span></tt></a> (0-based)</div></blockquote>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.index" title="MDAnalysis.core.AtomGroup.Atom.index"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.index</span></code></a> (0-based)</div></blockquote>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.Timestep.__eq__">
-<tt class="descname">__eq__</tt><big>(</big><em>other</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.__eq__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.__eq__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__eq__</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.__eq__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.__eq__" title="Permalink to this definition">¶</a></dt>
 <dd><p>Compare with another Timestep</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.Timestep.__iter__">
-<tt class="descname">__iter__</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.__iter__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.__iter__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__iter__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.__iter__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.__iter__" title="Permalink to this definition">¶</a></dt>
 <dd><p>Iterate over coordinates</p>
-<p><tt class="docutils literal"><span class="pre">for</span> <span class="pre">x</span> <span class="pre">in</span> <span class="pre">ts</span></tt></p>
+<p><code class="docutils literal"><span class="pre">for</span> <span class="pre">x</span> <span class="pre">in</span> <span class="pre">ts</span></code></p>
 <blockquote>
 <div>iterate of the coordinates, atom by atom</div></blockquote>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.Timestep.copy">
-<tt class="descname">copy</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.copy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>.</p>
+<code class="descname">copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.Timestep.copy_slice">
-<tt class="descname">copy_slice</tt><big>(</big><em>sel</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy_slice"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
+<code class="descname">copy_slice</code><span class="sig-paren">(</span><em>sel</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy_slice"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
 <dd><p>Make a new Timestep containing a subset of the original Timestep.</p>
-<p><tt class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></tt>
-<tt class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></tt></p>
+<p><code class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></code>
+<code class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></code></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A Timestep object of the same type containing all header
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A Timestep object of the same type containing all header
 information and all atom information relevant to the selection.</td>
 </tr>
 </tbody>
@@ -471,126 +487,137 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 <p class="last">The selection must be a 0 based slice or array of the atom indices
 in this Timestep</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
 copy official attributes of the Timestep.</p>
+</div>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.base.IObase">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.base.</tt><tt class="descname">IObase</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.base.</code><code class="descname">IObase</code><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase" title="Permalink to this definition">¶</a></dt>
 <dd><p>Base class bundling common functionality for trajectory I/O.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added context manager protocol.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added context manager protocol.</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.IObase.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.IObase.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_forces_from_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_forces_from_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.IObase.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_forces_to_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_forces_to_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.IObase.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_pos_from_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_pos_from_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.IObase.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_pos_to_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_pos_to_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.IObase.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_time_from_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_time_from_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.IObase.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_time_to_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_time_to_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.IObase.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_velocities_from_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_velocities_from_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.IObase.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_velocities_to_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#IObase.convert_velocities_to_native"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.IObase.format">
-<tt class="descname">format</tt><em class="property"> = None</em><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.format" title="Permalink to this definition">¶</a></dt>
+<code class="descname">format</code><em class="property"> = None</em><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.format" title="Permalink to this definition">¶</a></dt>
 <dd><p>override to define trajectory format of the reader/writer (DCD, XTC, ...)</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.IObase.units">
-<tt class="descname">units</tt><em class="property"> = {'velocity': None, 'length': None, 'time': None}</em><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.units" title="Permalink to this definition">¶</a></dt>
+<code class="descname">units</code><em class="property"> = {'velocity': None, 'length': None, 'time': None}</em><a class="headerlink" href="#MDAnalysis.coordinates.base.IObase.units" title="Permalink to this definition">¶</a></dt>
 <dd><p>dict with units of of <em>time</em> and <em>length</em> (and <em>velocity</em>, <em>force</em>,
 ... for formats that support it)</p>
 </dd></dl>
@@ -599,51 +626,53 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.base.Reader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.base.</tt><tt class="descname">Reader</tt><big>(</big><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Reader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Reader" title="Permalink to this definition">¶</a></dt>
-<dd><p>Base class for trajectory readers that extends <tt class="xref py py-class docutils literal"><span class="pre">ProtoReader</span></tt> with a <tt class="xref py py-meth docutils literal"><span class="pre">__del__()</span></tt> method.</p>
-<p>New Readers should subclass <a class="reference internal" href="#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><tt class="xref py py-class docutils literal"><span class="pre">Reader</span></tt></a> and properly implement a
-<tt class="xref py py-meth docutils literal"><span class="pre">close()</span></tt> method, to ensure proper release of resources (mainly file
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.base.</code><code class="descname">Reader</code><span class="sig-paren">(</span><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Reader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Reader" title="Permalink to this definition">¶</a></dt>
+<dd><p>Base class for trajectory readers that extends <code class="xref py py-class docutils literal"><span class="pre">ProtoReader</span></code> with a <code class="xref py py-meth docutils literal"><span class="pre">__del__()</span></code> method.</p>
+<p>New Readers should subclass <a class="reference internal" href="#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><code class="xref py py-class docutils literal"><span class="pre">Reader</span></code></a> and properly implement a
+<code class="xref py py-meth docutils literal"><span class="pre">close()</span></code> method, to ensure proper release of resources (mainly file
 handles). Readers that are inherently safe in this regard should subclass
-<tt class="xref py py-class docutils literal"><span class="pre">ProtoReader</span></tt> instead.</p>
-<p>See the <a class="reference internal" href="init.html#trajectory-api"><em>Trajectory API</em></a> definition in
-<a class="reference internal" href="init.html#module-MDAnalysis.coordinates.__init__" title="MDAnalysis.coordinates.__init__"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.__init__</span></tt></a> for the required attributes and
+<code class="xref py py-class docutils literal"><span class="pre">ProtoReader</span></code> instead.</p>
+<p>See the <a class="reference internal" href="init.html#trajectory-api"><span>Trajectory API</span></a> definition in
+<a class="reference internal" href="init.html#module-MDAnalysis.coordinates.__init__" title="MDAnalysis.coordinates.__init__"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.__init__</span></code></a> for the required attributes and
 methods.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-class docutils literal"><span class="pre">ProtoReader</span></tt></p>
+<p class="last"><code class="xref py py-class docutils literal"><span class="pre">ProtoReader</span></code></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Most of the base Reader class definitions were offloaded to
+<code class="xref py py-class docutils literal"><span class="pre">ProtoReader</span></code> so as to allow the subclassing of Readers without a
+<code class="xref py py-meth docutils literal"><span class="pre">__del__()</span></code> method.  Created init method to create common
+functionality, all Reader subclasses must now <a class="reference external" href="http://docs.python.org/library/functions.html#super" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">super()</span></code></a> through this
+class.  Added attribute <code class="xref py py-attr docutils literal"><span class="pre">_ts_kwargs</span></code>, which is created in init.
+Provides kwargs to be passed to <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a></p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Most of the base Reader class definitions were offloaded to
-<tt class="xref py py-class docutils literal"><span class="pre">ProtoReader</span></tt> so as to allow the subclassing of Readers without a
-<tt class="xref py py-meth docutils literal"><span class="pre">__del__()</span></tt> method.  Created init method to create common
-functionality, all Reader subclasses must now <a class="reference external" href="http://docs.python.org/library/functions.html#super" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">super()</span></tt></a> through this
-class.  Added attribute <tt class="xref py py-attr docutils literal"><span class="pre">_ts_kwargs</span></tt>, which is created in init.
-Provides kwargs to be passed to <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a></p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.base.ChainReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.base.</tt><tt class="descname">ChainReader</tt><big>(</big><em>filenames</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#ChainReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.ChainReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.base.</code><code class="descname">ChainReader</code><span class="sig-paren">(</span><em>filenames</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#ChainReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.ChainReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reader that concatenates multiple trajectories on the fly.</p>
 <p><strong>Known issues</strong></p>
 <ul class="simple">
 <li>Trajectory API attributes exist but most of them only reflect
-the first trajectory in the list; <tt class="xref py py-attr docutils literal"><span class="pre">ChainReader.n_frames</span></tt>,
-<tt class="xref py py-attr docutils literal"><span class="pre">ChainReader.n_atoms</span></tt>, and <tt class="xref py py-attr docutils literal"><span class="pre">ChainReader.fixed</span></tt> are
+the first trajectory in the list; <code class="xref py py-attr docutils literal"><span class="pre">ChainReader.n_frames</span></code>,
+<code class="xref py py-attr docutils literal"><span class="pre">ChainReader.n_atoms</span></code>, and <code class="xref py py-attr docutils literal"><span class="pre">ChainReader.fixed</span></code> are
 properly set, though</li>
 <li>slicing not implemented</li>
-<li><a class="reference internal" href="#MDAnalysis.coordinates.base.ChainReader.time" title="MDAnalysis.coordinates.base.ChainReader.time"><tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt></a> will not necessarily return the true time but just
+<li><a class="reference internal" href="#MDAnalysis.coordinates.base.ChainReader.time" title="MDAnalysis.coordinates.base.ChainReader.time"><code class="xref py py-attr docutils literal"><span class="pre">time</span></code></a> will not necessarily return the true time but just
 number of frames times a provided time between frames (from the
 keyword <em>delta</em>)</li>
 </ul>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 <p>Set up the chain reader.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filenames</em></dt>
 <dd><p class="first">file name or list of file names; the reader will open
 all file names and provide frames in the order of
@@ -661,8 +690,8 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 <dt><em>delta</em></dt>
 <dd><p class="first last">The time between frames in MDAnalysis time units if no
 other information is available. If this is not set then
-any call to <a class="reference internal" href="#MDAnalysis.coordinates.base.ChainReader.time" title="MDAnalysis.coordinates.base.ChainReader.time"><tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt></a> will raise a
-<tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt>.</p>
+any call to <a class="reference internal" href="#MDAnalysis.coordinates.base.ChainReader.time" title="MDAnalysis.coordinates.base.ChainReader.time"><code class="xref py py-attr docutils literal"><span class="pre">time</span></code></a> will raise a
+<code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code>.</p>
 </dd>
 <dt><em>kwargs</em></dt>
 <dd><p class="first last">all other keyword arguments are passed on to each
@@ -673,29 +702,30 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>The <em>delta</em> keyword was added.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>The <em>delta</em> keyword was added.</p>
+</div>
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.ChainReader.active_reader">
-<tt class="descname">active_reader</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#ChainReader.active_reader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.ChainReader.active_reader" title="Permalink to this definition">¶</a></dt>
+<code class="descname">active_reader</code><a class="headerlink" href="#MDAnalysis.coordinates.base.ChainReader.active_reader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reader instance from which frames are being read.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.ChainReader.frame">
-<tt class="descname">frame</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#ChainReader.frame"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.ChainReader.frame" title="Permalink to this definition">¶</a></dt>
+<code class="descname">frame</code><a class="headerlink" href="#MDAnalysis.coordinates.base.ChainReader.frame" title="Permalink to this definition">¶</a></dt>
 <dd><p>Cumulative frame number of the current time step.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.ChainReader.rewind">
-<tt class="descname">rewind</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#ChainReader.rewind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.ChainReader.rewind" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rewind</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#ChainReader.rewind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.ChainReader.rewind" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set current frame to the beginning.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.base.ChainReader.time">
-<tt class="descname">time</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#ChainReader.time"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.ChainReader.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.base.ChainReader.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>Cumulative time of the current frame in MDAnalysis time units (typically ps).</p>
 </dd></dl>
 
@@ -703,22 +733,22 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.base.Writer">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.base.</tt><tt class="descname">Writer</tt><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Writer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.base.</code><code class="descname">Writer</code><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Base class for trajectory writers.</p>
-<p>See Trajectory API definition in <a class="reference internal" href="init.html#module-MDAnalysis.coordinates.__init__" title="MDAnalysis.coordinates.__init__"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.__init__</span></tt></a> for
+<p>See Trajectory API definition in <a class="reference internal" href="init.html#module-MDAnalysis.coordinates.__init__" title="MDAnalysis.coordinates.__init__"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.__init__</span></code></a> for
 the required attributes and methods.</p>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.Writer.convert_dimensions_to_unitcell">
-<tt class="descname">convert_dimensions_to_unitcell</tt><big>(</big><em>ts</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Writer.convert_dimensions_to_unitcell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Writer.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_dimensions_to_unitcell</code><span class="sig-paren">(</span><em>ts</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Writer.convert_dimensions_to_unitcell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Writer.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read dimensions from timestep <em>ts</em> and return appropriate unitcell.</p>
-<p>The default is to return <tt class="docutils literal"><span class="pre">[A,B,C,alpha,beta,gamma]</span></tt>; if this
+<p>The default is to return <code class="docutils literal"><span class="pre">[A,B,C,alpha,beta,gamma]</span></code>; if this
 is not appropriate then this method has to be overriden.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.Writer.has_valid_coordinates">
-<tt class="descname">has_valid_coordinates</tt><big>(</big><em>criteria</em>, <em>x</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Writer.has_valid_coordinates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Writer.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns <tt class="docutils literal"><span class="pre">True</span></tt> if all values are within limit values of their formats.</p>
+<code class="descname">has_valid_coordinates</code><span class="sig-paren">(</span><em>criteria</em>, <em>x</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Writer.has_valid_coordinates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Writer.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns <code class="docutils literal"><span class="pre">True</span></code> if all values are within limit values of their formats.</p>
 <p>Due to rounding, the test is asymmetric (and <em>min</em> is supposed to be negative):</p>
 <blockquote>
 <div>min &lt; x &lt;= max</div></blockquote>
@@ -726,17 +756,17 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>criteria</em></dt>
 <dd><p class="first last">dictionary containing the <em>max</em> and <em>min</em> values in native units</p>
 </dd>
 <dt><em>x</em></dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></tt> of <tt class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></tt> coordinates of atoms selected to be written out.</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></code> of <code class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></code> coordinates of atoms selected to be written out.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">boolean</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">boolean</p>
 </td>
 </tr>
 </tbody>
@@ -745,10 +775,10 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.base.Writer.write">
-<tt class="descname">write</tt><big>(</big><em>obj</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Writer.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Writer.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/base.html#Writer.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.base.Writer.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write current timestep, using the supplied <em>obj</em>.</p>
-<p>The argument should be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> or
-a <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> or a <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance.</p>
+<p>The argument should be a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> or
+a <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> or a <a class="reference internal" href="#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The size of the <em>obj</em> must be the same as the number of atom
@@ -766,7 +796,7 @@ <h1>5.19. Base classes &#8212; <a class="reference internal" href="#module-MDAna
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -781,11 +811,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="TRZ.html" title="5.18. TRZ trajectory I/O — MDAnalysis.coordinates.TRZ"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -795,7 +825,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/core.html b/package/doc/html/documentation_pages/coordinates/core.html
index cca5581e282..990cbbd7488 100644
--- a/package/doc/html/documentation_pages/coordinates/core.html
+++ b/package/doc/html/documentation_pages/coordinates/core.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.20. Common functions for coordinate reading — MDAnalysis.coordinates.core &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.20. Common functions for coordinate reading — MDAnalysis.coordinates.core &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.21. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile" href="xdrfile.html" />
     <link rel="prev" title="5.19. Base classes — MDAnalysis.coordinates.base" href="base.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="base.html" title="5.19. Base classes — MDAnalysis.coordinates.base"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
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-                        title="previous chapter">5.19. Base classes &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></tt></a></p>
+                        title="previous chapter">5.19. Base classes &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></code></a></p>
   <h4>Next topic</h4>
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-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/core.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/core.txt"
+            rel="nofollow">Show Source</a></li>
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+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,41 +90,41 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.core"></span><div class="section" id="common-functions-for-coordinate-reading-mdanalysis-coordinates-core">
-<h1>5.20. Common functions for coordinate reading &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.core" title="MDAnalysis.coordinates.core"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.core</span></tt></a><a class="headerlink" href="#common-functions-for-coordinate-reading-mdanalysis-coordinates-core" title="Permalink to this headline">¶</a></h1>
-<p>Important base classes are collected in <a class="reference internal" href="base.html#module-MDAnalysis.coordinates.base" title="MDAnalysis.coordinates.base"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></tt></a>.</p>
+<h1>5.20. Common functions for coordinate reading &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.core" title="MDAnalysis.coordinates.core"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.core</span></code></a><a class="headerlink" href="#common-functions-for-coordinate-reading-mdanalysis-coordinates-core" title="Permalink to this headline">¶</a></h1>
+<p>Important base classes are collected in <a class="reference internal" href="base.html#module-MDAnalysis.coordinates.base" title="MDAnalysis.coordinates.base"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></code></a>.</p>
 <dl class="function">
 <dt id="MDAnalysis.coordinates.core.reader">
-<tt class="descclassname">MDAnalysis.coordinates.core.</tt><tt class="descname">reader</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/core.html#reader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.core.reader" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.core.</code><code class="descname">reader</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/core.html#reader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.core.reader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Provide a trajectory reader instance for <em>filename</em>.</p>
 <p>This function guesses the file format from the extension of <em>filename</em> and
-it will throw a <tt class="xref py py-exc docutils literal"><span class="pre">TypeError</span></tt> if the extension is not recognized.</p>
+it will throw a <code class="xref py py-exc docutils literal"><span class="pre">TypeError</span></code> if the extension is not recognized.</p>
 <p>In most cases, no special keyword arguments are necessary. For PDB readers
-it might be useful to set the <em>permissive</em> = <tt class="docutils literal"><span class="pre">True</span></tt> flag to
+it might be useful to set the <em>permissive</em> = <code class="docutils literal"><span class="pre">True</span></code> flag to
 select a simpler but faster reader.</p>
 <p>All other keywords are passed on to the underlying Reader classes; see
 their documentation for details.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last">For trajectory formats: <tt class="xref py py-class docutils literal"><span class="pre">DCDReader</span></tt>,
-<tt class="xref py py-class docutils literal"><span class="pre">XTCReader</span></tt>, <tt class="xref py py-class docutils literal"><span class="pre">TRRReader</span></tt>,
-<tt class="xref py py-class docutils literal"><span class="pre">XYZReader</span></tt>.  For single frame formats:
-<tt class="xref py py-class docutils literal"><span class="pre">CRDReader</span></tt>, <tt class="xref py py-class docutils literal"><span class="pre">PDBReader</span></tt> and
-<tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></tt>, <tt class="xref py py-class docutils literal"><span class="pre">GROReader</span></tt>,</p>
+<p class="last">For trajectory formats: <code class="xref py py-class docutils literal"><span class="pre">DCDReader</span></code>,
+<code class="xref py py-class docutils literal"><span class="pre">XTCReader</span></code>, <code class="xref py py-class docutils literal"><span class="pre">TRRReader</span></code>,
+<code class="xref py py-class docutils literal"><span class="pre">XYZReader</span></code>.  For single frame formats:
+<code class="xref py py-class docutils literal"><span class="pre">CRDReader</span></code>, <code class="xref py py-class docutils literal"><span class="pre">PDBReader</span></code> and
+<code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></code>, <code class="xref py py-class docutils literal"><span class="pre">GROReader</span></code>,</p>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the input trajectory or coordinate file</p>
 </dd>
 <dt><em>permissive</em></dt>
-<dd><p class="first last">If set to <tt class="docutils literal"><span class="pre">True</span></tt>, a reader is selected that is more tolerant of the
-input (currently only implemented for PDB). [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">If set to <code class="docutils literal"><span class="pre">True</span></code>, a reader is selected that is more tolerant of the
+input (currently only implemented for PDB). [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>kwargs</em></dt>
 <dd><p class="first last">Keyword arguments for the selected Reader class.</p>
@@ -138,13 +138,13 @@ <h1>5.20. Common functions for coordinate reading &#8212; <a class="reference in
 
 <dl class="function">
 <dt id="MDAnalysis.coordinates.core.writer">
-<tt class="descclassname">MDAnalysis.coordinates.core.</tt><tt class="descname">writer</tt><big>(</big><em>filename</em>, <em>n_atoms=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/core.html#writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.core.writer" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.core.</code><code class="descname">writer</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/core.html#writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.core.writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Initialize a trajectory writer instance for <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">Output filename of the trajectory; the extension determines the
 format.</p>
@@ -154,9 +154,9 @@ <h1>5.20. Common functions for coordinate reading &#8212; <a class="reference in
 for single-frame writers.</p>
 </dd>
 <dt><em>multiframe</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: write a trajectory with multiple frames; <tt class="docutils literal"><span class="pre">False</span></tt>
-only write a single frame snapshot; <tt class="docutils literal"><span class="pre">None</span></tt> first try to get
-a multiframe writer and then fall back to single frame [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: write a trajectory with multiple frames; <code class="docutils literal"><span class="pre">False</span></code>
+only write a single frame snapshot; <code class="docutils literal"><span class="pre">None</span></code> first try to get
+a multiframe writer and then fall back to single frame [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>kwargs</em></dt>
 <dd><p class="first">Keyword arguments for the writer; all trajectory Writers accept
@@ -176,11 +176,11 @@ <h1>5.20. Common functions for coordinate reading &#8212; <a class="reference in
 </div></blockquote>
 <p>Some readers accept additional arguments, which need to be looked
 up in the documentation of the reader.</p>
-<div class="admonition-see-also last admonition seealso">
+<div class="last admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="DCD.html#MDAnalysis.coordinates.DCD.DCDWriter" title="MDAnalysis.coordinates.DCD.DCDWriter"><tt class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></tt></a> for DCD
-trajectories or <a class="reference internal" href="XTC.html#MDAnalysis.coordinates.XTC.XTCWriter" title="MDAnalysis.coordinates.XTC.XTCWriter"><tt class="xref py py-class docutils literal"><span class="pre">XTCWriter</span></tt></a>
-and <a class="reference internal" href="TRR.html#MDAnalysis.coordinates.TRR.TRRWriter" title="MDAnalysis.coordinates.TRR.TRRWriter"><tt class="xref py py-class docutils literal"><span class="pre">TRRWriter</span></tt></a> for Gromacs.</p>
+<p class="last"><a class="reference internal" href="DCD.html#MDAnalysis.coordinates.DCD.DCDWriter" title="MDAnalysis.coordinates.DCD.DCDWriter"><code class="xref py py-class docutils literal"><span class="pre">DCDWriter</span></code></a> for DCD
+trajectories or <a class="reference internal" href="XTC.html#MDAnalysis.coordinates.XTC.XTCWriter" title="MDAnalysis.coordinates.XTC.XTCWriter"><code class="xref py py-class docutils literal"><span class="pre">XTCWriter</span></code></a>
+and <a class="reference internal" href="TRR.html#MDAnalysis.coordinates.TRR.TRRWriter" title="MDAnalysis.coordinates.TRR.TRRWriter"><code class="xref py py-class docutils literal"><span class="pre">TRRWriter</span></code></a> for Gromacs.</p>
 </div>
 </dd>
 </dl>
@@ -188,14 +188,15 @@ <h1>5.20. Common functions for coordinate reading &#8212; <a class="reference in
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>Added <em>multiframe</em> keyword. See also <a class="reference internal" href="#MDAnalysis.coordinates.core.get_writer_for" title="MDAnalysis.coordinates.core.get_writer_for"><tt class="xref py py-func docutils literal"><span class="pre">get_writer_for()</span></tt></a>.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>Added <em>multiframe</em> keyword. See also <a class="reference internal" href="#MDAnalysis.coordinates.core.get_writer_for" title="MDAnalysis.coordinates.core.get_writer_for"><code class="xref py py-func docutils literal"><span class="pre">get_writer_for()</span></code></a>.</p>
+</div>
 </dd></dl>
 
 <p>Helper functions:</p>
 <dl class="function">
 <dt id="MDAnalysis.coordinates.core.get_reader_for">
-<tt class="descclassname">MDAnalysis.coordinates.core.</tt><tt class="descname">get_reader_for</tt><big>(</big><em>filename</em>, <em>permissive=False</em>, <em>format=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/core.html#get_reader_for"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.core.get_reader_for" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.core.</code><code class="descname">get_reader_for</code><span class="sig-paren">(</span><em>filename</em>, <em>permissive=False</em>, <em>format=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/core.html#get_reader_for"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.core.get_reader_for" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return the appropriate trajectory reader class for <em>filename</em>.</p>
 <p>Automatic detection is disabled when an explicit <em>format</em> is
 provided.</p>
@@ -203,18 +204,18 @@ <h1>5.20. Common functions for coordinate reading &#8212; <a class="reference in
 
 <dl class="function">
 <dt id="MDAnalysis.coordinates.core.get_writer_for">
-<tt class="descclassname">MDAnalysis.coordinates.core.</tt><tt class="descname">get_writer_for</tt><big>(</big><em>filename=None</em>, <em>format='DCD'</em>, <em>multiframe=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/core.html#get_writer_for"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.core.get_writer_for" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.core.</code><code class="descname">get_writer_for</code><span class="sig-paren">(</span><em>filename=None</em>, <em>format='DCD'</em>, <em>multiframe=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/core.html#get_writer_for"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.core.get_writer_for" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return an appropriate trajectory or frame writer class for <em>filename</em>.</p>
 <p>The format is determined by the <em>format</em> argument or the extension of
 <em>filename</em>. The default is to return a dcd writer (<em>format</em> = &#8216;dcd&#8217;). If
 the <em>filename</em> is not provided or if it is something like a
-<tt class="xref py py-class docutils literal"><span class="pre">cStringIO.StringIO</span></tt> instance then the <em>format</em> argument must be
+<code class="xref py py-class docutils literal"><span class="pre">cStringIO.StringIO</span></code> instance then the <em>format</em> argument must be
 used.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">The filename for the trajectory is examined for its extension and
 the Writer is chosen accordingly.</p>
@@ -224,30 +225,19 @@ <h1>5.20. Common functions for coordinate reading &#8212; <a class="reference in
 possible values are &#8220;DCD&#8221;, &#8220;XTC&#8221;, &#8220;TRR&#8221;; &#8220;PDB&#8221;, &#8220;CRD&#8221;, &#8220;GRO&#8221;.</p>
 </dd>
 <dt><em>multiframe</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: write multiple frames to the trajectory; <tt class="docutils literal"><span class="pre">False</span></tt>: only
-write a single coordinate frame; <tt class="docutils literal"><span class="pre">None</span></tt>: first try trajectory (multi
-frame writers), then the single frame ones. Default is <tt class="docutils literal"><span class="pre">None</span></tt>.</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: write multiple frames to the trajectory; <code class="docutils literal"><span class="pre">False</span></code>: only
+write a single coordinate frame; <code class="docutils literal"><span class="pre">None</span></code>: first try trajectory (multi
+frame writers), then the single frame ones. Default is <code class="docutils literal"><span class="pre">None</span></code>.</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>Added <em>multiframe</em> keyword; the default <tt class="docutils literal"><span class="pre">None</span></tt> reflects the previous
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>Added <em>multiframe</em> keyword; the default <code class="docutils literal"><span class="pre">None</span></code> reflects the previous
 behaviour.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="MDAnalysis.coordinates.core.guess_format">
-<tt class="descclassname">MDAnalysis.coordinates.core.</tt><tt class="descname">guess_format</tt><big>(</big><em>filename</em>, <em>format=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/core.html#guess_format"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.core.guess_format" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns the type of file <em>filename</em>.</p>
-<p>The current heuristic simply looks at the filename extension but more
-complicated probes could be implemented here or in the individual packages
-(e.g. as static methods). <em>filename</em> can also be a stream, in which case
-<em>filename.name</em> is looked at for a hint to the format if <em>format</em> is not
-provided.</p>
-<p>If <em>format</em> is supplied then it overrides the auto detection.</p>
+</div>
 </dd></dl>
 
 </div>
@@ -258,7 +248,7 @@ <h1>5.20. Common functions for coordinate reading &#8212; <a class="reference in
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -273,11 +263,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="base.html" title="5.19. Base classes — MDAnalysis.coordinates.base"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -287,7 +277,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/init.html b/package/doc/html/documentation_pages/coordinates/init.html
index 41622d19fbb..6befbd07f12 100644
--- a/package/doc/html/documentation_pages/coordinates/init.html
+++ b/package/doc/html/documentation_pages/coordinates/init.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.1. Trajectory Readers and Writers — MDAnalysis.coordinates &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.1. Trajectory Readers and Writers — MDAnalysis.coordinates &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.2. CRD structure files in MDAnalysis — MDAnalysis.coordinates.CRD" href="CRD.html" />
     <link rel="prev" title="5. Coordinates modules" href="../coordinates_modules.html" /> 
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+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
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   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.1. Trajectory Readers and Writers  &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.1. Trajectory Readers and Writers  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates</span></code></a><ul>
 <li><a class="reference internal" href="#readers">5.1.1. Readers</a></li>
 <li><a class="reference internal" href="#writers">5.1.2. Writers</a></li>
 <li><a class="reference internal" href="#timesteps">5.1.3. Timesteps</a></li>
@@ -102,13 +100,15 @@ <h4>Previous topic</h4>
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   <span class="target" id="module-MDAnalysis.coordinates.__init__"></span><div class="section" id="trajectory-readers-and-writers-mdanalysis-coordinates">
-<h1>5.1. Trajectory Readers and Writers  &#8212; <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates</span></tt><a class="headerlink" href="#trajectory-readers-and-writers-mdanalysis-coordinates" title="Permalink to this headline">¶</a></h1>
+<h1>5.1. Trajectory Readers and Writers  &#8212; <code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates</span></code><a class="headerlink" href="#trajectory-readers-and-writers-mdanalysis-coordinates" title="Permalink to this headline">¶</a></h1>
 <p>The coordinates submodule contains code to read, write and store coordinate
 information,
 either single frames (e.g. the GRO module) or trajectories (such as the DCD
 reader).</p>
 <div class="section" id="readers">
 <h2>5.1.1. Readers<a class="headerlink" href="#readers" title="Permalink to this headline">¶</a></h2>
-<p>All Readers are supposed to expose a <tt class="xref py py-class docutils literal"><span class="pre">ProtoReader</span></tt> object
+<p>All Readers are supposed to expose a <code class="xref py py-class docutils literal"><span class="pre">ProtoReader</span></code> object
 that presents a common <a class="reference internal" href="#trajectory-api">Trajectory API</a> to other code.</p>
-<p>The <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> contains the API
+<p>The <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> contains the API
 entry point attribute</p>
 <blockquote>
-<div><tt class="xref py py-attr docutils literal"><span class="pre">Universe.trajectory</span></tt></div></blockquote>
-<p>that points to the actual <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><tt class="xref py py-class docutils literal"><span class="pre">Reader</span></tt></a>
+<div><code class="xref py py-attr docutils literal"><span class="pre">Universe.trajectory</span></code></div></blockquote>
+<p>that points to the actual <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><code class="xref py py-class docutils literal"><span class="pre">Reader</span></code></a>
 object; all Readers are supposed to be accessible through this entry
 point in the same manner (&#8220;<a class="reference external" href="http://c2.com/cgi/wiki?DuckTyping">duck typing</a>&#8221;).</p>
 <p>There are three types of base Reader which act as starting points
 for each specific format. These are:</p>
 <dl class="docutils">
-<dt><a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><tt class="xref py py-class docutils literal"><span class="pre">Reader</span></tt></a></dt>
+<dt><a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><code class="xref py py-class docutils literal"><span class="pre">Reader</span></code></a></dt>
 <dd>A standard multi frame Reader which allows iteration over a single
 file to provide multiple frames of data.  This is used by formats
 such as TRR and DCD.</dd>
-<dt><tt class="xref py py-class docutils literal"><span class="pre">SingleFrameReader</span></tt></dt>
+<dt><code class="xref py py-class docutils literal"><span class="pre">SingleFrameReader</span></code></dt>
 <dd>A simplified Reader which reads a file containing only a single
 frame of information.  This is used with formats such as GRO
 and CRD</dd>
-<dt><tt class="xref py py-class docutils literal"><span class="pre">baseChainReader</span></tt></dt>
+<dt><code class="xref py py-class docutils literal"><span class="pre">baseChainReader</span></code></dt>
 <dd>An advanced Reader designed to read a sequence of files, to
 provide iteration over all the frames in each file seamlessly.
 This Reader can also provide this functionality over a
 sequence of files in different formats.</dd>
 </dl>
 <p>Normally, one does not explicitly need to select a reader. This is handled
-automatically when creating a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> and
+automatically when creating a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> and
 the appropriate reader for the file type is selected (typically by the file
-extension but this choice can be overriden with the <tt class="docutils literal"><span class="pre">format</span></tt> argument to
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>).</p>
+extension but this choice can be overriden with the <code class="docutils literal"><span class="pre">format</span></code> argument to
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>).</p>
 </div>
 <div class="section" id="writers">
 <h2>5.1.2. Writers<a class="headerlink" href="#writers" title="Permalink to this headline">¶</a></h2>
 <p>In order to <strong>write coordinates</strong>, a factory function is provided
-(<a class="reference internal" href="core.html#MDAnalysis.coordinates.core.writer" title="MDAnalysis.coordinates.core.writer"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.coordinates.core.writer()</span></tt></a>) which is made available
-as <tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></tt>) that returns a <em>Writer</em> appropriate for
+(<a class="reference internal" href="core.html#MDAnalysis.coordinates.core.writer" title="MDAnalysis.coordinates.core.writer"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.coordinates.core.writer()</span></code></a>) which is made available
+as <code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></code>) that returns a <em>Writer</em> appropriate for
 the desired file format (as indicated by the filename
 suffix). Furthermore, a trajectory
-<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><tt class="xref py py-class docutils literal"><span class="pre">Reader</span></tt></a> can also have a method
-<tt class="xref py py-meth docutils literal"><span class="pre">Writer()</span></tt> that returns an
-appropriate <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Writer" title="MDAnalysis.coordinates.base.Writer"><tt class="xref py py-class docutils literal"><span class="pre">Writer</span></tt></a> for the file
+<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><code class="xref py py-class docutils literal"><span class="pre">Reader</span></code></a> can also have a method
+<code class="xref py py-meth docutils literal"><span class="pre">Writer()</span></code> that returns an
+appropriate <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Writer" title="MDAnalysis.coordinates.base.Writer"><code class="xref py py-class docutils literal"><span class="pre">Writer</span></code></a> for the file
 format of the trajectory.</p>
-<p>In analogy to <a class="reference internal" href="core.html#MDAnalysis.coordinates.core.writer" title="MDAnalysis.coordinates.core.writer"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.coordinates.core.writer()</span></tt></a>, there is
-also a <a class="reference internal" href="core.html#MDAnalysis.coordinates.core.reader" title="MDAnalysis.coordinates.core.reader"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.coordinates.core.reader()</span></tt></a> function available
-to return a trajectory <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><tt class="xref py py-class docutils literal"><span class="pre">Reader</span></tt></a>
+<p>In analogy to <a class="reference internal" href="core.html#MDAnalysis.coordinates.core.writer" title="MDAnalysis.coordinates.core.writer"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.coordinates.core.writer()</span></code></a>, there is
+also a <a class="reference internal" href="core.html#MDAnalysis.coordinates.core.reader" title="MDAnalysis.coordinates.core.reader"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.coordinates.core.reader()</span></code></a> function available
+to return a trajectory <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><code class="xref py py-class docutils literal"><span class="pre">Reader</span></code></a>
 instance although this is often not needed because the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> class can choose an
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> class can choose an
 appropriate reader automatically.</p>
 <p>A typical approach is to generate a new trajectory from an old one, e.g. to
 only keep the protein:</p>
@@ -195,17 +195,17 @@ <h2>5.1.2. Writers<a class="headerlink" href="#writers" title="Permalink to this
         <span class="n">W</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">protein</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>Using the <tt class="xref py py-func docutils literal"><span class="pre">with()</span></tt> statement will automatically close the trajectory when
+<p>Using the <code class="xref py py-func docutils literal"><span class="pre">with()</span></code> statement will automatically close the trajectory when
 the last frame has been written.</p>
 </div>
 <div class="section" id="timesteps">
 <h2>5.1.3. Timesteps<a class="headerlink" href="#timesteps" title="Permalink to this headline">¶</a></h2>
 <p>Both Readers and Writers use Timesteps as their working object.  A Timestep
 represents all data for a given frame in a trajectory.  The data inside a
-Timestep is often accessed indirectly through a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
+Timestep is often accessed indirectly through a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
 but it is also possible to manipulate Timesteps directly.</p>
 <p>The current Timestep can be accessed through the trajectory read attached
-to the active <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a></p>
+to the active <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a></p>
 <blockquote>
 <div>ts = u.trajectory.ts
 ts.positions  # returns a numpy array of positions</div></blockquote>
@@ -221,12 +221,12 @@ <h2>5.1.4. Supported coordinate formats<a class="headerlink" href="#supported-co
 default, MDAnalysis figures out formats by looking at the extension. Thus, a
 DCD file always has to end with &#8221;.dcd&#8221; to be recognized as such unless the
 format is explicitly specified with the <em>format</em> keyword to
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> or
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.load_new" title="MDAnalysis.core.AtomGroup.Universe.load_new"><tt class="xref py py-meth docutils literal"><span class="pre">load_new()</span></tt></a>.  A number of files are
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> or
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.load_new" title="MDAnalysis.core.AtomGroup.Universe.load_new"><code class="xref py py-meth docutils literal"><span class="pre">load_new()</span></code></a>.  A number of files are
 also recognized when they are compressed with <strong class="program">gzip</strong> or
 <strong class="program">bzip2</strong> such as &#8221;.xyz.bz2&#8221;.</p>
-<table border="1" class="docutils" id="id1">
-<caption>Table of supported coordinate formats</caption>
+<table border="1" class="docutils" id="id18">
+<span id="id1"></span><caption><span class="caption-text">Table of supported coordinate formats</span><a class="headerlink" href="#id18" title="Permalink to this table">¶</a></caption>
 <colgroup>
 <col width="17%" />
 <col width="13%" />
@@ -248,14 +248,14 @@ <h2>5.1.4. Supported coordinate formats<a class="headerlink" href="#supported-co
 <td>standard CHARMM binary trajectory; endianness is
 autodetected. Fixed atoms may not be handled
 correctly (requires testing). Module
-<a class="reference internal" href="DCD.html#module-MDAnalysis.coordinates.DCD" title="MDAnalysis.coordinates.DCD"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></tt></a></td>
+<a class="reference internal" href="DCD.html#module-MDAnalysis.coordinates.DCD" title="MDAnalysis.coordinates.DCD"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>LAMMPS</td>
 <td>dcd</td>
 <td>r/w</td>
 <td>CHARMM-style binary trajectory; endianness is
 autodetected. Units are appropriate for LAMMPS.
-Module <a class="reference internal" href="LAMMPS.html#module-MDAnalysis.coordinates.LAMMPS" title="MDAnalysis.coordinates.LAMMPS"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></tt></a></td>
+Module <a class="reference internal" href="LAMMPS.html#module-MDAnalysis.coordinates.LAMMPS" title="MDAnalysis.coordinates.LAMMPS"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></code></a></td>
 </tr>
 <tr class="row-even"><td>LAMMPS <a class="footnote-reference" href="#a" id="id2">[1]</a></td>
 <td>data</td>
@@ -266,21 +266,21 @@ <h2>5.1.4. Supported coordinate formats<a class="headerlink" href="#supported-co
 <td>xtc</td>
 <td>r/w</td>
 <td>Compressed (lossy) xtc trajectory format. Module
-<a class="reference internal" href="XTC.html#module-MDAnalysis.coordinates.XTC" title="MDAnalysis.coordinates.XTC"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></tt></a></td>
+<a class="reference internal" href="XTC.html#module-MDAnalysis.coordinates.XTC" title="MDAnalysis.coordinates.XTC"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></code></a></td>
 </tr>
 <tr class="row-even"><td>Gromacs</td>
 <td>trr</td>
 <td>r/w</td>
 <td>Full precision trr trajectory. Coordinates and
 velocities are processed. Module
-<a class="reference internal" href="TRR.html#module-MDAnalysis.coordinates.TRR" title="MDAnalysis.coordinates.TRR"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRR</span></tt></a></td>
+<a class="reference internal" href="TRR.html#module-MDAnalysis.coordinates.TRR" title="MDAnalysis.coordinates.TRR"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRR</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>XYZ <a class="footnote-reference" href="#a" id="id3">[1]</a></td>
 <td>xyz</td>
 <td>r/w</td>
 <td>Generic white-space separate XYZ format; can be
 compressed (gzip or bzip2). Module
-<a class="reference internal" href="XYZ.html#module-MDAnalysis.coordinates.XYZ" title="MDAnalysis.coordinates.XYZ"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.XYZ</span></tt></a></td>
+<a class="reference internal" href="XYZ.html#module-MDAnalysis.coordinates.XYZ" title="MDAnalysis.coordinates.XYZ"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.XYZ</span></code></a></td>
 </tr>
 <tr class="row-even"><td>GAMESS</td>
 <td>gms,
@@ -289,7 +289,7 @@ <h2>5.1.4. Supported coordinate formats<a class="headerlink" href="#supported-co
 <td>r</td>
 <td>Generic semi-formatted GAMESS output log; can be
 compressed (gzip or bzip2). Module
-<a class="reference internal" href="GMS.html#module-MDAnalysis.coordinates.GMS" title="MDAnalysis.coordinates.GMS"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.GMS</span></tt></a></td>
+<a class="reference internal" href="GMS.html#module-MDAnalysis.coordinates.GMS" title="MDAnalysis.coordinates.GMS"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.GMS</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>AMBER</td>
 <td>trj,
@@ -297,21 +297,21 @@ <h2>5.1.4. Supported coordinate formats<a class="headerlink" href="#supported-co
 <td>r</td>
 <td>formatted (ASCII) trajectories; the presence of a
 periodic box is autodetected (<em>experimental</em>).
-Module <a class="reference internal" href="TRJ.html#module-MDAnalysis.coordinates.TRJ" title="MDAnalysis.coordinates.TRJ"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></tt></a></td>
+Module <a class="reference internal" href="TRJ.html#module-MDAnalysis.coordinates.TRJ" title="MDAnalysis.coordinates.TRJ"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></code></a></td>
 </tr>
 <tr class="row-even"><td>AMBER</td>
 <td>inpcrd
 restrt</td>
 <td>r</td>
 <td>formatted (ASCII) coordinate/restart file
-Module <a class="reference internal" href="INPCRD.html#module-MDAnalysis.coordinates.INPCRD" title="MDAnalysis.coordinates.INPCRD"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.INPCRD</span></tt></a></td>
+Module <a class="reference internal" href="INPCRD.html#module-MDAnalysis.coordinates.INPCRD" title="MDAnalysis.coordinates.INPCRD"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.INPCRD</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>AMBER</td>
 <td>ncdf</td>
 <td>r/w</td>
 <td>binary (NetCDF) trajectories are fully supported with
 optional <a class="reference external" href="https://github.com/Unidata/netcdf4-python">netcdf4-python</a> module (coordinates and
-velocities). Module <a class="reference internal" href="TRJ.html#module-MDAnalysis.coordinates.TRJ" title="MDAnalysis.coordinates.TRJ"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></tt></a></td>
+velocities). Module <a class="reference internal" href="TRJ.html#module-MDAnalysis.coordinates.TRJ" title="MDAnalysis.coordinates.TRJ"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></code></a></td>
 </tr>
 <tr class="row-even"><td>Brookhaven
 <a class="footnote-reference" href="#a" id="id4">[1]</a></td>
@@ -320,38 +320,38 @@ <h2>5.1.4. Supported coordinate formats<a class="headerlink" href="#supported-co
 <td>a simplified PDB format (as used in MD simulations)
 is read by default; the full format can be read by
 supplying the <cite>permissive=False</cite> flag to
-<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt>. Multiple frames (MODEL)
+<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code>. Multiple frames (MODEL)
 are supported but require the <em>multiframe</em> keyword.
-Module <a class="reference internal" href="PDB.html#module-MDAnalysis.coordinates.PDB" title="MDAnalysis.coordinates.PDB"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></tt></a></td>
+Module <a class="reference internal" href="PDB.html#module-MDAnalysis.coordinates.PDB" title="MDAnalysis.coordinates.PDB"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>XPDB</td>
 <td>pdb</td>
 <td>r</td>
 <td>Extended PDB format (can use 5-digit residue
 numbers). To use, specify the format &#8220;XPBD&#8221;
-explicitly: <tt class="docutils literal"><span class="pre">Universe(...,</span> <span class="pre">format=&quot;XPDB&quot;)</span></tt>.
-Module <a class="reference internal" href="PDB.html#module-MDAnalysis.coordinates.PDB" title="MDAnalysis.coordinates.PDB"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></tt></a></td>
+explicitly: <code class="docutils literal"><span class="pre">Universe(...,</span> <span class="pre">format=&quot;XPDB&quot;)</span></code>.
+Module <a class="reference internal" href="PDB.html#module-MDAnalysis.coordinates.PDB" title="MDAnalysis.coordinates.PDB"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></code></a></td>
 </tr>
 <tr class="row-even"><td>PDBQT <a class="footnote-reference" href="#a" id="id5">[1]</a></td>
 <td>pdbqt</td>
 <td>r/w</td>
 <td>file format used by AutoDock with atom types <em>t</em>
 and partial charges <em>q</em>. Module:
-<a class="reference internal" href="PDBQT.html#module-MDAnalysis.coordinates.PDBQT" title="MDAnalysis.coordinates.PDBQT"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDBQT</span></tt></a></td>
+<a class="reference internal" href="PDBQT.html#module-MDAnalysis.coordinates.PDBQT" title="MDAnalysis.coordinates.PDBQT"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDBQT</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>PQR <a class="footnote-reference" href="#a" id="id6">[1]</a></td>
 <td>pqr</td>
 <td>r/w</td>
 <td>PDB-like but whitespace-separated files with charge
 and radius information. Module
-<a class="reference internal" href="PQR.html#module-MDAnalysis.coordinates.PQR" title="MDAnalysis.coordinates.PQR"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PQR</span></tt></a></td>
+<a class="reference internal" href="PQR.html#module-MDAnalysis.coordinates.PQR" title="MDAnalysis.coordinates.PQR"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PQR</span></code></a></td>
 </tr>
 <tr class="row-even"><td>GROMOS96
 <a class="footnote-reference" href="#a" id="id7">[1]</a></td>
 <td>gro</td>
 <td>r/w</td>
 <td>basic GROMOS96 format (velocities as well). Module
-<a class="reference internal" href="GRO.html#module-MDAnalysis.coordinates.GRO" title="MDAnalysis.coordinates.GRO"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></tt></a></td>
+<a class="reference internal" href="GRO.html#module-MDAnalysis.coordinates.GRO" title="MDAnalysis.coordinates.GRO"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>CHARMM
 CARD <a class="footnote-reference" href="#a" id="id8">[1]</a></td>
@@ -359,37 +359,37 @@ <h2>5.1.4. Supported coordinate formats<a class="headerlink" href="#supported-co
 <td>r/w</td>
 <td>&#8220;CARD&#8221; coordinate output from CHARMM; deals with
 either standard or EXTended format. Module
-<a class="reference internal" href="CRD.html#module-MDAnalysis.coordinates.CRD" title="MDAnalysis.coordinates.CRD"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.CRD</span></tt></a></td>
+<a class="reference internal" href="CRD.html#module-MDAnalysis.coordinates.CRD" title="MDAnalysis.coordinates.CRD"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.CRD</span></code></a></td>
 </tr>
 <tr class="row-even"><td>DESRES <a class="footnote-reference" href="#a" id="id9">[1]</a></td>
 <td>dms</td>
 <td>r</td>
 <td>DESRES Molecular Structure file format reader.
-Module <a class="reference internal" href="DMS.html#module-MDAnalysis.coordinates.DMS" title="MDAnalysis.coordinates.DMS"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DMS</span></tt></a></td>
+Module <a class="reference internal" href="DMS.html#module-MDAnalysis.coordinates.DMS" title="MDAnalysis.coordinates.DMS"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DMS</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>IBIsCO/YASP</td>
 <td>trz</td>
 <td>r/w</td>
 <td>Binary IBIsCO or YASP trajectories Module
-<a class="reference internal" href="TRZ.html#module-MDAnalysis.coordinates.TRZ" title="MDAnalysis.coordinates.TRZ"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRZ</span></tt></a></td>
+<a class="reference internal" href="TRZ.html#module-MDAnalysis.coordinates.TRZ" title="MDAnalysis.coordinates.TRZ"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRZ</span></code></a></td>
 </tr>
 <tr class="row-even"><td>MOL2</td>
 <td>mol2</td>
 <td>r/w</td>
 <td>Text-based Tripos molecular structure format
-<a class="reference internal" href="MOL2.html#module-MDAnalysis.coordinates.MOL2" title="MDAnalysis.coordinates.MOL2"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></tt></a></td>
+<a class="reference internal" href="MOL2.html#module-MDAnalysis.coordinates.MOL2" title="MDAnalysis.coordinates.MOL2"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>DL_Poly <a class="footnote-reference" href="#a" id="id10">[1]</a></td>
 <td>config</td>
 <td>r</td>
 <td>DL_Poly ascii config file
-<tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DLPOLY</span></tt></td>
+<code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DLPOLY</span></code></td>
 </tr>
 <tr class="row-even"><td>DL_Poly <a class="footnote-reference" href="#a" id="id11">[1]</a></td>
 <td>history</td>
 <td>r</td>
 <td>DL_Poly ascii history file
-<tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DLPOLY</span></tt></td>
+<code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.DLPOLY</span></code></td>
 </tr>
 </tbody>
 </table>
@@ -398,8 +398,8 @@ <h2>5.1.4. Supported coordinate formats<a class="headerlink" href="#supported-co
 <tbody valign="top">
 <tr><td class="label">[1]</td><td><em>(<a class="fn-backref" href="#id2">1</a>, <a class="fn-backref" href="#id3">2</a>, <a class="fn-backref" href="#id4">3</a>, <a class="fn-backref" href="#id5">4</a>, <a class="fn-backref" href="#id6">5</a>, <a class="fn-backref" href="#id7">6</a>, <a class="fn-backref" href="#id8">7</a>, <a class="fn-backref" href="#id9">8</a>, <a class="fn-backref" href="#id10">9</a>, <a class="fn-backref" href="#id11">10</a>)</em> This format can also be used to provide basic <em>topology</em>
 information (i.e. the list of atoms); it is possible to create a
-full <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-mod docutils literal"><span class="pre">Universe</span></tt></a> by simply
-providing a file of this format: <tt class="docutils literal"><span class="pre">u</span> <span class="pre">=</span> <span class="pre">Universe(filename)</span></tt></td></tr>
+full <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-mod docutils literal"><span class="pre">Universe</span></code></a> by simply
+providing a file of this format: <code class="docutils literal"><span class="pre">u</span> <span class="pre">=</span> <span class="pre">Universe(filename)</span></code></td></tr>
 </tbody>
 </table>
 </div>
@@ -412,7 +412,7 @@ <h2>5.1.4. Supported coordinate formats<a class="headerlink" href="#supported-co
 <p>Typically, each format resides in its own module, named by the format specifier
 (and using upper case by convention).</p>
 <p>Reader and Writer classes are derived from base classes in
-<a class="reference internal" href="base.html#module-MDAnalysis.coordinates.base" title="MDAnalysis.coordinates.base"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></tt></a>.</p>
+<a class="reference internal" href="base.html#module-MDAnalysis.coordinates.base" title="MDAnalysis.coordinates.base"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></code></a>.</p>
 <div class="section" id="history">
 <h3>5.1.5.1. History<a class="headerlink" href="#history" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
@@ -427,7 +427,7 @@ <h3>5.1.5.1. History<a class="headerlink" href="#history" title="Permalink to th
 <li>2011-04-20 added volume to Timestep</li>
 <li>2012-02-11 added _velocities to Timestep</li>
 <li>2012-05-24 multiframe keyword to distinguish trajectory from single frame writers</li>
-<li>2012-06-04 missing implementations of Reader.__getitem__ should raise <tt class="xref py py-exc docutils literal"><span class="pre">TypeError</span></tt></li>
+<li>2012-06-04 missing implementations of Reader.__getitem__ should raise <code class="xref py py-exc docutils literal"><span class="pre">TypeError</span></code></li>
 <li>2013-08-02 Readers/Writers must conform to the Python <a class="reference external" href="http://docs.python.org/2/reference/datamodel.html#context-managers">Context Manager</a> API</li>
 <li>2015-01-15 Timestep._init_unitcell() method added</li>
 <li>2015-06-11 Reworked Timestep init.  Base Timestep now does Vels &amp; Forces</li>
@@ -442,11 +442,11 @@ <h3>5.1.5.2. Registry<a class="headerlink" href="#registry" title="Permalink to
 with the format (typically the file extension in upper case):</p>
 <ul class="simple">
 <li>Trajectory reader classes must be added to
-<tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.coordinates._trajectory_readers</span></tt>.</li>
+<code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.coordinates._trajectory_readers</span></code>.</li>
 <li>Trajectory writer classes must be added to
-<tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.coordinates._trajectory_writers</span></tt>.</li>
+<code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.coordinates._trajectory_writers</span></code>.</li>
 <li>Single-frame writer classes must be added to to
-<tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.coordinates._frame_writers</span></tt>.</li>
+<code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.coordinates._frame_writers</span></code>.</li>
 </ul>
 </div>
 <div class="section" id="timestep-class">
@@ -454,31 +454,31 @@ <h3>5.1.5.2. Registry<a class="headerlink" href="#registry" title="Permalink to
 <p>A Timestep instance holds data for the current frame. It is updated whenever a
 new frame of the trajectory is read.</p>
 <p>Timestep classes are derived from
-<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep</span></tt></a>, which is the primary
+<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep</span></code></a>, which is the primary
 implementation example (and used directly for the DCDReader).</p>
 <p>The discussion on this format is detailed in <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/issues/250">Issue 250</a></p>
 <div class="section" id="methods">
 <h4>5.1.5.3.1. Methods<a class="headerlink" href="#methods" title="Permalink to this headline">¶</a></h4>
 <blockquote>
 <div><dl class="docutils">
-<dt><tt class="docutils literal"><span class="pre">__init__(n_atoms,</span> <span class="pre">positions=True,</span> <span class="pre">velocities=False,</span> <span class="pre">forces=False)</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__init__(n_atoms,</span> <span class="pre">positions=True,</span> <span class="pre">velocities=False,</span> <span class="pre">forces=False)</span></code></dt>
 <dd>Define the number of atoms this Timestep will hold and whether or not
 it will have velocity and force information</dd>
-<dt><tt class="docutils literal"><span class="pre">__eq__</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__eq__</span></code></dt>
 <dd>Compares a Timestep with another</dd>
-<dt><tt class="docutils literal"><span class="pre">__getitem__(atoms)</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__getitem__(atoms)</span></code></dt>
 <dd>position(s) of atoms; can be a slice or numpy array and then returns
 coordinate array</dd>
-<dt><tt class="docutils literal"><span class="pre">__len__()</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__len__()</span></code></dt>
 <dd>number of coordinates (atoms) in the frame</dd>
-<dt><tt class="docutils literal"><span class="pre">__iter__()</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__iter__()</span></code></dt>
 <dd>iterator over all coordinates</dd>
-<dt><tt class="docutils literal"><span class="pre">copy()</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">copy()</span></code></dt>
 <dd>deep copy of the instance</dd>
-<dt><tt class="docutils literal"><span class="pre">_init_unitcell</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">_init_unitcell</span></code></dt>
 <dd>hook that returns empty data structure for the unitcell representation
-of this particular file format; called from within <tt class="docutils literal"><span class="pre">__init__()</span></tt> to
-initialize <tt class="xref py py-attr docutils literal"><span class="pre">Timestep._unitcell</span></tt>.</dd>
+of this particular file format; called from within <code class="docutils literal"><span class="pre">__init__()</span></code> to
+initialize <code class="xref py py-attr docutils literal"><span class="pre">Timestep._unitcell</span></code>.</dd>
 </dl>
 </div></blockquote>
 </div>
@@ -486,52 +486,52 @@ <h4>5.1.5.3.1. Methods<a class="headerlink" href="#methods" title="Permalink to
 <h4>5.1.5.3.2. Attributes<a class="headerlink" href="#attributes" title="Permalink to this headline">¶</a></h4>
 <blockquote>
 <div><dl class="docutils">
-<dt><tt class="docutils literal"><span class="pre">n_atoms</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">n_atoms</span></code></dt>
 <dd>number of atoms in the frame</dd>
-<dt><tt class="docutils literal"><span class="pre">frame</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">frame</span></code></dt>
 <dd>current frame number (0-based)</dd>
-<dt><tt class="docutils literal"><span class="pre">_frame</span></tt></dt>
-<dd>The native frame number of the trajectory.  This can differ from <tt class="docutils literal"><span class="pre">frame</span></tt>
+<dt><code class="docutils literal"><span class="pre">_frame</span></code></dt>
+<dd>The native frame number of the trajectory.  This can differ from <code class="docutils literal"><span class="pre">frame</span></code>
 as that will always count sequentially from 0 on iteration, whilst
-<tt class="docutils literal"><span class="pre">_frame</span></tt> is taken directly from the trajectory.</dd>
-<dt><tt class="docutils literal"><span class="pre">time</span></tt></dt>
+<code class="docutils literal"><span class="pre">_frame</span></code> is taken directly from the trajectory.</dd>
+<dt><code class="docutils literal"><span class="pre">time</span></code></dt>
 <dd>The current system time in ps.  This value is calculated either from a time
 set as the Timestep attribute, or from <cite>frame</cite> * <cite>dt</cite>.  Either method allows
 allows an offset to be applied to the time.</dd>
-<dt><tt class="docutils literal"><span class="pre">dt</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">dt</span></code></dt>
 <dd>The change in system time between different frames.  This can be set as an
 attribute, but defaults to 1.0 ps.</dd>
-<dt><tt class="docutils literal"><span class="pre">data</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">data</span></code></dt>
 <dd>A dictionary containing all miscellaneous information for the
 current Timestep.</dd>
-<dt><tt class="docutils literal"><span class="pre">positions</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">positions</span></code></dt>
 <dd>A numpy array of all positions in this Timestep, otherwise raises a
-<a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><tt class="xref py py-class docutils literal"><span class="pre">NoDataError</span></tt></a></dd>
-<dt><tt class="docutils literal"><span class="pre">velocities</span></tt></dt>
+<a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><code class="xref py py-class docutils literal"><span class="pre">NoDataError</span></code></a></dd>
+<dt><code class="docutils literal"><span class="pre">velocities</span></code></dt>
 <dd>If present, returns a numpy array of velocities, otherwise raises a
-<a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><tt class="xref py py-class docutils literal"><span class="pre">NoDataError</span></tt></a></dd>
-<dt><tt class="docutils literal"><span class="pre">forces</span></tt></dt>
+<a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><code class="xref py py-class docutils literal"><span class="pre">NoDataError</span></code></a></dd>
+<dt><code class="docutils literal"><span class="pre">forces</span></code></dt>
 <dd>If present, returns a numpy array of forces, otherwise raises a
-<a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><tt class="xref py py-class docutils literal"><span class="pre">NoDataError</span></tt></a></dd>
-<dt><tt class="docutils literal"><span class="pre">has_positions</span></tt></dt>
+<a class="reference internal" href="../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><code class="xref py py-class docutils literal"><span class="pre">NoDataError</span></code></a></dd>
+<dt><code class="docutils literal"><span class="pre">has_positions</span></code></dt>
 <dd>Boolean of whether position data is available</dd>
-<dt><tt class="docutils literal"><span class="pre">has_velocities</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">has_velocities</span></code></dt>
 <dd>Boolean of whether velocity data is available</dd>
-<dt><tt class="docutils literal"><span class="pre">has_forces</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">has_forces</span></code></dt>
 <dd>Boolean of whether force data is available</dd>
-<dt><tt class="docutils literal"><span class="pre">dimensions</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">dimensions</span></code></dt>
 <dd><p class="first">system box dimensions (<cite>x, y, z, alpha, beta, gamma</cite>)
 (typically implemented as a property because it needs to translate whatever is in the
-underlying <tt class="xref py py-class docutils literal"><span class="pre">_unitcell</span></tt> attribute. Also
+underlying <code class="xref py py-class docutils literal"><span class="pre">_unitcell</span></code> attribute. Also
 comes with a setter that takes a MDAnalysis box so that one can do</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">Timestep</span><span class="o">.</span><span class="n">dimensions</span> <span class="o">=</span> <span class="p">[</span><span class="n">A</span><span class="p">,</span> <span class="n">B</span><span class="p">,</span> <span class="n">C</span><span class="p">,</span> <span class="n">alpha</span><span class="p">,</span> <span class="n">beta</span><span class="p">,</span> <span class="n">gamma</span><span class="p">]</span>
 </pre></div>
 </div>
 <p class="last">which then converts automatically to the underlying representation and stores it
-in <tt class="xref py py-attr docutils literal"><span class="pre">Timestep._unitcell</span></tt>.</p>
+in <code class="xref py py-attr docutils literal"><span class="pre">Timestep._unitcell</span></code>.</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">volume</span></tt></dt>
-<dd>system box volume (derived as the determinant of the box vectors of <tt class="docutils literal"><span class="pre">dimensions</span></tt>)</dd>
+<dt><code class="docutils literal"><span class="pre">volume</span></code></dt>
+<dd>system box volume (derived as the determinant of the box vectors of <code class="docutils literal"><span class="pre">dimensions</span></code>)</dd>
 </dl>
 </div></blockquote>
 </div>
@@ -542,21 +542,21 @@ <h4>5.1.5.3.3. Private attributes<a class="headerlink" href="#private-attributes
 but instead should use the attribute above.</p>
 <blockquote>
 <div><dl class="docutils">
-<dt><tt class="docutils literal"><span class="pre">_pos</span></tt></dt>
-<dd>raw coordinates, a <tt class="xref py py-class docutils literal"><span class="pre">numpy.float32</span></tt> array; <tt class="docutils literal"><span class="pre">X</span> <span class="pre">=</span> <span class="pre">_pos[:,0],</span> <span class="pre">Y</span> <span class="pre">=</span>
-<span class="pre">_pos[:,1],</span> <span class="pre">Z</span> <span class="pre">=</span> <span class="pre">_pos[:,2]</span></tt></dd>
-<dt><tt class="docutils literal"><span class="pre">_velocities</span></tt></dt>
-<dd>raw velocities, a <tt class="xref py py-class docutils literal"><span class="pre">numpy.float32</span></tt> array containing velocities
-(similar to <tt class="docutils literal"><span class="pre">_pos</span></tt>)</dd>
-<dt><tt class="docutils literal"><span class="pre">_forces</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">_pos</span></code></dt>
+<dd>raw coordinates, a <code class="xref py py-class docutils literal"><span class="pre">numpy.float32</span></code> array; <code class="docutils literal"><span class="pre">X</span> <span class="pre">=</span> <span class="pre">_pos[:,0],</span> <span class="pre">Y</span> <span class="pre">=</span>
+<span class="pre">_pos[:,1],</span> <span class="pre">Z</span> <span class="pre">=</span> <span class="pre">_pos[:,2]</span></code></dd>
+<dt><code class="docutils literal"><span class="pre">_velocities</span></code></dt>
+<dd>raw velocities, a <code class="xref py py-class docutils literal"><span class="pre">numpy.float32</span></code> array containing velocities
+(similar to <code class="docutils literal"><span class="pre">_pos</span></code>)</dd>
+<dt><code class="docutils literal"><span class="pre">_forces</span></code></dt>
 <dd>forces, similar to velocities above.</dd>
-<dt><tt class="docutils literal"><span class="pre">_unitcell</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">_unitcell</span></code></dt>
 <dd><p class="first">native unit cell description; the format depends on the
 underlying trajectory format. A user should use the
-<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-class docutils literal"><span class="pre">dimensions</span></tt></a>
+<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-class docutils literal"><span class="pre">dimensions</span></code></a>
 attribute to access the data in a canonical format instead of
-accessing <tt class="xref py py-class docutils literal"><span class="pre">Timestep._unitcell</span></tt> directly.</p>
-<p class="last">The method <tt class="xref py py-meth docutils literal"><span class="pre">Timestep._init_unitcell()</span></tt> is a hook to initialize
+accessing <code class="xref py py-class docutils literal"><span class="pre">Timestep._unitcell</span></code> directly.</p>
+<p class="last">The method <code class="xref py py-meth docutils literal"><span class="pre">Timestep._init_unitcell()</span></code> is a hook to initialize
 this attribute.</p>
 </dd>
 </dl>
@@ -565,55 +565,55 @@ <h4>5.1.5.3.3. Private attributes<a class="headerlink" href="#private-attributes
 </div>
 <div class="section" id="trajectory-reader-class">
 <h3>5.1.5.4. Trajectory Reader class<a class="headerlink" href="#trajectory-reader-class" title="Permalink to this headline">¶</a></h3>
-<p>Trajectory readers are derived from <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Reader</span></tt></a>.
+<p>Trajectory readers are derived from <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Reader</span></code></a>.
 Typically, many methods and attributes are overriden.</p>
 <div class="section" id="id13">
 <h4>5.1.5.4.1. Methods<a class="headerlink" href="#id13" title="Permalink to this headline">¶</a></h4>
-<p>The <a class="reference internal" href="DCD.html#MDAnalysis.coordinates.DCD.DCDReader" title="MDAnalysis.coordinates.DCD.DCDReader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.DCD.DCDReader</span></tt></a> class is the primary
+<p>The <a class="reference internal" href="DCD.html#MDAnalysis.coordinates.DCD.DCDReader" title="MDAnalysis.coordinates.DCD.DCDReader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.DCD.DCDReader</span></code></a> class is the primary
 implementation example.</p>
 <p><strong>Mandatory methods</strong></p>
 <p>The following methods must be implemented in a Reader class.</p>
 <blockquote>
 <div><dl class="docutils">
-<dt><tt class="docutils literal"><span class="pre">__init__(filename,</span> <span class="pre">**kwargs)</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__init__(filename,</span> <span class="pre">**kwargs)</span></code></dt>
 <dd><p class="first">open <em>filename</em>; other <em>kwargs</em> are processed as needed and the
 Reader is free to ignore them. Typically, MDAnalysis supplies as
 much information as possible to the Reader in <cite>kwargs</cite>; at the moment the
 following data are supplied in keywords when a trajectory is loaded from
-within <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt>:</p>
+within <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code>:</p>
 <blockquote class="last">
 <div><ul class="simple">
 <li><em>n_atoms</em>: the number of atoms (known from the topology)</li>
 </ul>
 </div></blockquote>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">__iter__()</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__iter__()</span></code></dt>
 <dd><p class="first">allow iteration from beginning to end:</p>
 <div class="last highlight-python"><div class="highlight"><pre><span class="k">for</span> <span class="n">ts</span> <span class="ow">in</span> <span class="n">trajectory</span><span class="p">:</span>
     <span class="k">print</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span>
 </pre></div>
 </div>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">close()</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">close()</span></code></dt>
 <dd>close the file and cease I/O</dd>
-<dt><tt class="docutils literal"><span class="pre">next()</span></tt></dt>
-<dd>advance to next time step or raise <tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> when moving
+<dt><code class="docutils literal"><span class="pre">next()</span></code></dt>
+<dd>advance to next time step or raise <code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> when moving
 past the last frame</dd>
-<dt><tt class="docutils literal"><span class="pre">rewind()</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">rewind()</span></code></dt>
 <dd>reposition to first frame</dd>
-<dt><tt class="docutils literal"><span class="pre">__entry__()</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__entry__()</span></code></dt>
 <dd>entry method of a <a class="reference external" href="http://docs.python.org/2/reference/datamodel.html#context-managers">Context Manager</a> (returns self)</dd>
-<dt><tt class="docutils literal"><span class="pre">__exit__()</span></tt></dt>
-<dd>exit method of a <a class="reference external" href="http://docs.python.org/2/reference/datamodel.html#context-managers">Context Manager</a>, should call <tt class="docutils literal"><span class="pre">close()</span></tt>.</dd>
+<dt><code class="docutils literal"><span class="pre">__exit__()</span></code></dt>
+<dd>exit method of a <a class="reference external" href="http://docs.python.org/2/reference/datamodel.html#context-managers">Context Manager</a>, should call <code class="docutils literal"><span class="pre">close()</span></code>.</dd>
 </dl>
 </div></blockquote>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">a <tt class="docutils literal"><span class="pre">__del__()</span></tt> method should also be present to ensure that the
+<p class="last">a <code class="docutils literal"><span class="pre">__del__()</span></code> method should also be present to ensure that the
 trajectory is properly closed. However, certain types of Reader can ignore
-this requirement. These include the <tt class="xref py py-class docutils literal"><span class="pre">SingleFrameReader</span></tt> (file reading
-is done within a context manager and needs no closing by hand) and the <tt class="xref py py-class docutils literal"><span class="pre">ChainReader</span></tt>
-(it is a collection of Readers, each already with its own <tt class="docutils literal"><span class="pre">__del__</span></tt> method).</p>
+this requirement. These include the <code class="xref py py-class docutils literal"><span class="pre">SingleFrameReader</span></code> (file reading
+is done within a context manager and needs no closing by hand) and the <code class="xref py py-class docutils literal"><span class="pre">ChainReader</span></code>
+(it is a collection of Readers, each already with its own <code class="docutils literal"><span class="pre">__del__</span></code> method).</p>
 </div>
 <p><strong>Optional methods</strong></p>
 <p>Not all trajectory formats support the following methods, either because the
@@ -621,17 +621,17 @@ <h4>5.1.5.4.1. Methods<a class="headerlink" href="#id13" title="Permalink to thi
 deal with missing methods gracefully.</p>
 <blockquote>
 <div><dl class="docutils">
-<dt><tt class="docutils literal"><span class="pre">__len__()</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__len__()</span></code></dt>
 <dd>number of frames in trajectory</dd>
-<dt><tt class="docutils literal"><span class="pre">__getitem__(arg)</span></tt></dt>
-<dd><p class="first">advance to time step <cite>arg</cite> = <cite>frame</cite> and return <tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt>; or if <cite>arg</cite> is a
+<dt><code class="docutils literal"><span class="pre">__getitem__(arg)</span></code></dt>
+<dd><p class="first">advance to time step <cite>arg</cite> = <cite>frame</cite> and return <code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code>; or if <cite>arg</cite> is a
 slice, then return an iterator over that part of the trajectory.</p>
 <p>The first functionality allows one to randomly access frames in the
 trajectory:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">universe</span><span class="o">.</span><span class="n">trajectory</span><span class="p">[</span><span class="mi">314</span><span class="p">]</span>
 </pre></div>
 </div>
-<p>would load frame 314 into the current <tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt>.</p>
+<p>would load frame 314 into the current <code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code>.</p>
 <p>Using slices allows iteration over parts of a trajectory</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="k">for</span> <span class="n">ts</span> <span class="ow">in</span> <span class="n">universe</span><span class="o">.</span><span class="n">trajectory</span><span class="p">[</span><span class="mi">1000</span><span class="p">:</span><span class="mi">2000</span><span class="p">]:</span>
     <span class="n">process_frame</span><span class="p">(</span><span class="n">ts</span><span class="p">)</span>   <span class="c"># do some analysis on ts</span>
@@ -644,31 +644,31 @@ <h4>5.1.5.4.1. Methods<a class="headerlink" href="#id13" title="Permalink to thi
 </div>
 <p>The last example starts reading the trajectory at frame 1000 and
 reads every 100th frame until the end.</p>
-<p>The performance of the <tt class="docutils literal"><span class="pre">__getitem__()</span></tt> method depends on the underlying
+<p>The performance of the <code class="docutils literal"><span class="pre">__getitem__()</span></code> method depends on the underlying
 trajectory reader and if it can implement random access to frames. In many
 cases this is not easily (or reliably) implementable and thus one is
 restricted to sequential iteration.</p>
 <p class="last">If the Reader is not able to provide random access to frames then it
-should raise <tt class="xref py py-exc docutils literal"><span class="pre">TypeError</span></tt> on indexing. It is possible to partially
-implement <tt class="docutils literal"><span class="pre">__getitem__</span></tt> (as done on
-<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Reader.__getitem__</span></tt> where slicing the
+should raise <code class="xref py py-exc docutils literal"><span class="pre">TypeError</span></code> on indexing. It is possible to partially
+implement <code class="docutils literal"><span class="pre">__getitem__</span></code> (as done on
+<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Reader.__getitem__</span></code> where slicing the
 full trajectory is equivalent to
-<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Reader.__iter__</span></tt> (which is always
-implemented) and other slices raise <tt class="xref py py-exc docutils literal"><span class="pre">TypeError</span></tt>.</p>
+<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Reader.__iter__</span></code> (which is always
+implemented) and other slices raise <code class="xref py py-exc docutils literal"><span class="pre">TypeError</span></code>.</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">Writer(filename,</span> <span class="pre">**kwargs)</span></tt></dt>
-<dd><p class="first">returns a <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Writer" title="MDAnalysis.coordinates.base.Writer"><tt class="xref py py-class docutils literal"><span class="pre">Writer</span></tt></a> which is set up with
+<dt><code class="docutils literal"><span class="pre">Writer(filename,</span> <span class="pre">**kwargs)</span></code></dt>
+<dd><p class="first">returns a <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Writer" title="MDAnalysis.coordinates.base.Writer"><code class="xref py py-class docutils literal"><span class="pre">Writer</span></code></a> which is set up with
 the same parameters as the trajectory that is being read (e.g. time step,
 length etc), which facilitates copying and simple on-the-fly manipulation.</p>
-<p>If no Writer is defined then a <tt class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></tt> is raised.</p>
+<p>If no Writer is defined then a <code class="xref py py-exc docutils literal"><span class="pre">NotImplementedError</span></code> is raised.</p>
 <p class="last">The <em>kwargs</em> can be used to customize the Writer as they are typically
 passed through to the init method of the Writer, with sensible defaults
 filled in; the actual keyword arguments depend on the Writer.</p>
 </dd>
-<dt><tt class="docutils literal"><span class="pre">timeseries(atomGroup,</span> <span class="pre">[start[,stop[,skip[,format]]]])</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">timeseries(atomGroup,</span> <span class="pre">[start[,stop[,skip[,format]]]])</span></code></dt>
 <dd>returns a subset of coordinate data</dd>
-<dt><tt class="docutils literal"><span class="pre">correl(timeseriesCollection[,start[,stop[,skip]]])</span></tt></dt>
-<dd>populate a <a class="reference internal" href="../core/Timeseries.html#MDAnalysis.core.Timeseries.TimeseriesCollection" title="MDAnalysis.core.Timeseries.TimeseriesCollection"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.Timeseries.TimeseriesCollection</span></tt></a> object
+<dt><code class="docutils literal"><span class="pre">correl(timeseriesCollection[,start[,stop[,skip]]])</span></code></dt>
+<dd>populate a <a class="reference internal" href="../core/Timeseries.html#MDAnalysis.core.Timeseries.TimeseriesCollection" title="MDAnalysis.core.Timeseries.TimeseriesCollection"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.Timeseries.TimeseriesCollection</span></code></a> object
 with observable timeseries computed from the trajectory</dd>
 </dl>
 </div></blockquote>
@@ -677,49 +677,49 @@ <h4>5.1.5.4.1. Methods<a class="headerlink" href="#id13" title="Permalink to thi
 <h4>5.1.5.4.2. Attributes<a class="headerlink" href="#id14" title="Permalink to this headline">¶</a></h4>
 <blockquote>
 <div><dl class="docutils">
-<dt><tt class="docutils literal"><span class="pre">filename</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">filename</span></code></dt>
 <dd>filename of the trajectory</dd>
-<dt><tt class="docutils literal"><span class="pre">n_atoms</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">n_atoms</span></code></dt>
 <dd>number of atoms (coordinate sets) in a frame (constant)</dd>
-<dt><tt class="docutils literal"><span class="pre">n_frames</span></tt></dt>
-<dd>total number of frames (if known) &#8211; <tt class="docutils literal"><span class="pre">None</span></tt> if not known</dd>
-<dt><tt class="docutils literal"><span class="pre">ts</span></tt></dt>
-<dd>the <tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt> object; typically customized for each
-trajectory format and derived from <tt class="xref py py-class docutils literal"><span class="pre">base.Timestep</span></tt>.</dd>
-<dt><tt class="docutils literal"><span class="pre">units</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">n_frames</span></code></dt>
+<dd>total number of frames (if known) &#8211; <code class="docutils literal"><span class="pre">None</span></code> if not known</dd>
+<dt><code class="docutils literal"><span class="pre">ts</span></code></dt>
+<dd>the <code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code> object; typically customized for each
+trajectory format and derived from <code class="xref py py-class docutils literal"><span class="pre">base.Timestep</span></code>.</dd>
+<dt><code class="docutils literal"><span class="pre">units</span></code></dt>
 <dd>dictionary with keys <em>time</em>, <em>length</em>, <em>speed</em>, <em>force</em> and the
 appropriate unit (e.g. &#8216;AKMA&#8217; and &#8216;Angstrom&#8217; for Charmm dcds, &#8216;ps&#8217; and
-&#8216;nm&#8217; for Gromacs trajectories, <tt class="docutils literal"><span class="pre">None</span></tt> and &#8216;Angstrom&#8217; for PDB).
-Any field not used should be set to <tt class="docutils literal"><span class="pre">None</span></tt>.</dd>
-<dt><tt class="docutils literal"><span class="pre">format</span></tt></dt>
+&#8216;nm&#8217; for Gromacs trajectories, <code class="docutils literal"><span class="pre">None</span></code> and &#8216;Angstrom&#8217; for PDB).
+Any field not used should be set to <code class="docutils literal"><span class="pre">None</span></code>.</dd>
+<dt><code class="docutils literal"><span class="pre">format</span></code></dt>
 <dd>string that identifies the file format, e.g. &#8220;DCD&#8221;, &#8220;PDB&#8221;, &#8220;CRD&#8221;, &#8220;XTC&#8221;,
 &#8220;TRR&#8221;; this is typically the file extension in upper case.</dd>
-<dt><tt class="docutils literal"><span class="pre">dt</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">dt</span></code></dt>
 <dd>time between frames in ps; a managed attribute (read only) that computes
-on the fly <tt class="docutils literal"><span class="pre">skip_timestep</span> <span class="pre">*</span> <span class="pre">delta</span></tt> and converts to the MDAnalysis base
+on the fly <code class="docutils literal"><span class="pre">skip_timestep</span> <span class="pre">*</span> <span class="pre">delta</span></code> and converts to the MDAnalysis base
 unit for time (pico seconds by default)</dd>
-<dt><tt class="docutils literal"><span class="pre">totaltime</span></tt></dt>
-<dd>total length of the trajectory = <tt class="docutils literal"><span class="pre">n_frames</span> <span class="pre">*</span> <span class="pre">dt</span></tt></dd>
-<dt><tt class="docutils literal"><span class="pre">time</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">totaltime</span></code></dt>
+<dd>total length of the trajectory = <code class="docutils literal"><span class="pre">n_frames</span> <span class="pre">*</span> <span class="pre">dt</span></code></dd>
+<dt><code class="docutils literal"><span class="pre">time</span></code></dt>
 <dd>time of the current time step, in MDAnalysis time units (ps)</dd>
-<dt><tt class="docutils literal"><span class="pre">frame</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">frame</span></code></dt>
 <dd>frame number of the current time step (0-based)</dd>
 </dl>
 </div></blockquote>
 <p><strong>Optional attributes</strong></p>
 <blockquote>
 <div><dl class="docutils">
-<dt><tt class="docutils literal"><span class="pre">delta</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">delta</span></code></dt>
 <dd>integrator time step (in native units); hence the &#8220;length&#8221;
-of a trajctory frame is  <tt class="docutils literal"><span class="pre">skip_timestep*delta</span></tt> time units</dd>
-<dt><tt class="docutils literal"><span class="pre">compressed</span></tt></dt>
-<dd>string that identifies the compression (e.g. &#8220;gz&#8221; or &#8220;bz2&#8221;) or <tt class="docutils literal"><span class="pre">None</span></tt>.</dd>
-<dt><tt class="docutils literal"><span class="pre">fixed</span></tt></dt>
+of a trajctory frame is  <code class="docutils literal"><span class="pre">skip_timestep*delta</span></code> time units</dd>
+<dt><code class="docutils literal"><span class="pre">compressed</span></code></dt>
+<dd>string that identifies the compression (e.g. &#8220;gz&#8221; or &#8220;bz2&#8221;) or <code class="docutils literal"><span class="pre">None</span></code>.</dd>
+<dt><code class="docutils literal"><span class="pre">fixed</span></code></dt>
 <dd>bool, saying if there are fixed atoms (e.g. dcds)</dd>
-<dt><tt class="docutils literal"><span class="pre">periodic</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">periodic</span></code></dt>
 <dd>boolean saying if contains box information for periodic boundary conditions
 unit cell information is stored in attribute <cite>dimensions</cite></dd>
-<dt><tt class="docutils literal"><span class="pre">skip_timestep</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">skip_timestep</span></code></dt>
 <dd>number of integrator steps between frames + 1 (i.e.
 the stride at which the MD simulation was sampled)</dd>
 </dl>
@@ -729,9 +729,9 @@ <h4>5.1.5.4.2. Attributes<a class="headerlink" href="#id14" title="Permalink to
 <div class="section" id="trajectory-writer-class">
 <h3>5.1.5.5. Trajectory Writer class<a class="headerlink" href="#trajectory-writer-class" title="Permalink to this headline">¶</a></h3>
 <p>Trajectory writers are derived from
-<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Writer" title="MDAnalysis.coordinates.base.Writer"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Writer</span></tt></a>. They are used to write
+<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Writer" title="MDAnalysis.coordinates.base.Writer"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Writer</span></code></a>. They are used to write
 multiple frames to a trajectory file. Every time the
-<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Writer.write" title="MDAnalysis.coordinates.base.Writer.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a> method is called,
+<a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Writer.write" title="MDAnalysis.coordinates.base.Writer.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a> method is called,
 another frame is appended to the trajectory.</p>
 <p>Typically, many methods and attributes are overriden.</p>
 <p>Signature:</p>
@@ -749,18 +749,18 @@ <h3>5.1.5.5. Trajectory Writer class<a class="headerlink" href="#trajectory-writ
 <h4>5.1.5.5.1. Methods<a class="headerlink" href="#id15" title="Permalink to this headline">¶</a></h4>
 <blockquote>
 <div><dl class="docutils">
-<dt><tt class="docutils literal"><span class="pre">__init__(filename,n_atoms[,start[,step[,delta[,remarks]]]])</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__init__(filename,n_atoms[,start[,step[,delta[,remarks]]]])</span></code></dt>
 <dd>opens <em>filename</em> and writes header if required by format</dd>
-<dt><tt class="docutils literal"><span class="pre">write(obj)</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">write(obj)</span></code></dt>
 <dd>write Timestep data in <em>obj</em></dd>
-<dt><tt class="docutils literal"><span class="pre">write_next_timestep([timestep])</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">write_next_timestep([timestep])</span></code></dt>
 <dd>write data in <em>timestep</em> to trajectory file</dd>
-<dt><tt class="docutils literal"><span class="pre">convert_dimensions_to_unitcell(timestep)</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">convert_dimensions_to_unitcell(timestep)</span></code></dt>
 <dd>take the dimensions from the timestep and convert to the native
 unitcell representation of the format</dd>
-<dt><tt class="docutils literal"><span class="pre">close()</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">close()</span></code></dt>
 <dd>close file and finish I/O</dd>
-<dt><tt class="docutils literal"><span class="pre">__del__()</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__del__()</span></code></dt>
 <dd>ensures that close() is called</dd>
 </dl>
 </div></blockquote>
@@ -769,16 +769,16 @@ <h4>5.1.5.5.1. Methods<a class="headerlink" href="#id15" title="Permalink to thi
 <h4>5.1.5.5.2. Attributes<a class="headerlink" href="#id16" title="Permalink to this headline">¶</a></h4>
 <blockquote>
 <div><dl class="docutils">
-<dt><tt class="docutils literal"><span class="pre">filename</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">filename</span></code></dt>
 <dd>name of the trajectory file</dd>
-<dt><tt class="docutils literal"><span class="pre">start,</span> <span class="pre">stop,</span> <span class="pre">step</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">start,</span> <span class="pre">stop,</span> <span class="pre">step</span></code></dt>
 <dd>first and last frame number (0-based) and step</dd>
-<dt><tt class="docutils literal"><span class="pre">units</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">units</span></code></dt>
 <dd>dictionary with keys <em>time</em>, <em>length</em>, <em>speed</em>, <em>force</em> and the
 appropriate unit (e.g. &#8216;AKMA&#8217; and &#8216;Angstrom&#8217; for Charmm dcds, &#8216;ps&#8217; and
-&#8216;nm&#8217; for Gromacs trajectories, <tt class="docutils literal"><span class="pre">None</span></tt> and &#8216;Angstrom&#8217; for PDB).
-Any field not used should be set to <tt class="docutils literal"><span class="pre">None</span></tt>.</dd>
-<dt><tt class="docutils literal"><span class="pre">format</span></tt></dt>
+&#8216;nm&#8217; for Gromacs trajectories, <code class="docutils literal"><span class="pre">None</span></code> and &#8216;Angstrom&#8217; for PDB).
+Any field not used should be set to <code class="docutils literal"><span class="pre">None</span></code>.</dd>
+<dt><code class="docutils literal"><span class="pre">format</span></code></dt>
 <dd>string that identifies the file format, e.g. &#8220;DCD&#8221;, &#8220;PDB&#8221;, &#8220;CRD&#8221;, &#8220;XTC&#8221;,
 &#8220;TRR&#8221;</dd>
 </dl>
@@ -786,8 +786,8 @@ <h4>5.1.5.5.2. Attributes<a class="headerlink" href="#id16" title="Permalink to
 <p><strong>Optional</strong></p>
 <blockquote>
 <div><dl class="docutils">
-<dt><tt class="docutils literal"><span class="pre">ts</span></tt></dt>
-<dd><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt> instance</dd>
+<dt><code class="docutils literal"><span class="pre">ts</span></code></dt>
+<dd><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code> instance</dd>
 </dl>
 </div></blockquote>
 </div>
@@ -808,18 +808,18 @@ <h3>5.1.5.6. Single Frame Writer class<a class="headerlink" href="#single-frame-
 </div>
 <p>The blanket <em>kwargs</em> is required so that one can pass the same kind of
 arguments (filename and n_atoms) as for the Trajectory writers. In
-this way, the simple <a class="reference internal" href="core.html#MDAnalysis.coordinates.core.writer" title="MDAnalysis.coordinates.core.writer"><tt class="xref py py-func docutils literal"><span class="pre">writer()</span></tt></a>
+this way, the simple <a class="reference internal" href="core.html#MDAnalysis.coordinates.core.writer" title="MDAnalysis.coordinates.core.writer"><code class="xref py py-func docutils literal"><span class="pre">writer()</span></code></a>
 factory function can be used for all writers.</p>
 <div class="section" id="id17">
 <h4>5.1.5.6.1. Methods<a class="headerlink" href="#id17" title="Permalink to this headline">¶</a></h4>
 <blockquote>
 <div><dl class="docutils">
-<dt><tt class="docutils literal"><span class="pre">__init__(filename,</span> <span class="pre">**kwargs)</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">__init__(filename,</span> <span class="pre">**kwargs)</span></code></dt>
 <dd>opens <em>filename</em> for writing; <cite>kwargs</cite> are typically ignored</dd>
-<dt><tt class="docutils literal"><span class="pre">write(obj)</span></tt></dt>
+<dt><code class="docutils literal"><span class="pre">write(obj)</span></code></dt>
 <dd>writes the object <em>obj</em>, containing a
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> group of atoms (typically
-obtained from a selection) or <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> group of atoms (typically
+obtained from a selection) or <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>
 to the file and closes the file</dd>
 </dl>
 </div></blockquote>
@@ -827,7 +827,7 @@ <h4>5.1.5.6.1. Methods<a class="headerlink" href="#id17" title="Permalink to thi
 <p class="first admonition-title">Note</p>
 <p class="last">Trajectory and Frame writers can be used in almost exactly the same
 manner with the one difference that Frame writers cannot deal with
-raw <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects.</p>
+raw <a class="reference internal" href="base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects.</p>
 </div>
 </div>
 </div>
@@ -840,30 +840,30 @@ <h2>5.1.6. Reader/Writer registry<a class="headerlink" href="#reader-writer-regi
 directly.</p>
 <p>Some formats can either write single frames or trajectories (such as
 PDB). In theses cases, the kind of writer is selected with the
-<em>multiframe</em> keyword to <tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.coordinates.core.get_writer()</span></tt>
+<em>multiframe</em> keyword to <code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.coordinates.core.get_writer()</span></code>
 (or the writer itself).</p>
 <dl class="data">
 <dt id="MDAnalysis.coordinates.__init__._trajectory_readers">
-<tt class="descclassname">MDAnalysis.coordinates.__init__.</tt><tt class="descname">_trajectory_readers</tt><em class="property"> = {'DMS': &lt;class 'MDAnalysis.coordinates.DMS.DMSReader'&gt;, 'CRD': &lt;class 'MDAnalysis.coordinates.CRD.CRDReader'&gt;, 'DATA': &lt;class 'MDAnalysis.coordinates.LAMMPS.DATAReader'&gt;, 'XPDB': &lt;class 'MDAnalysis.coordinates.PDB.ExtendedPDBReader'&gt;, 'CHAIN': &lt;class 'MDAnalysis.coordinates.base.ChainReader'&gt;, 'DCD': &lt;class 'MDAnalysis.coordinates.DCD.DCDReader'&gt;, 'NC': &lt;class 'MDAnalysis.coordinates.TRJ.NCDFReader'&gt;, 'TRJ': &lt;class 'MDAnalysis.coordinates.TRJ.TRJReader'&gt;, 'MDCRD': &lt;class 'MDAnalysis.coordinates.TRJ.TRJReader'&gt;, 'TRZ': &lt;class 'MDAnalysis.coordinates.TRZ.TRZReader'&gt;, 'XTC': &lt;class 'MDAnalysis.coordinates.xdrfile.XTC.XTCReader'&gt;, 'GMS': &lt;class 'MDAnalysis.coordinates.GMS.GMSReader'&gt;, 'GRO': &lt;class 'MDAnalysis.coordinates.GRO.GROReader'&gt;, 'TRR': &lt;class 'MDAnalysis.coordinates.xdrfile.TRR.TRRReader'&gt;, 'PDB': &lt;class 'MDAnalysis.coordinates.PDB.PDBReader'&gt;, 'HISTORY': &lt;class 'MDAnalysis.coordinates.DLPoly.HistoryReader'&gt;, 'LAMMPS': &lt;class 'MDAnalysis.coordinates.LAMMPS.DCDReader'&gt;, 'Permissive_PDB': &lt;class 'MDAnalysis.coordinates.PDB.PrimitivePDBReader'&gt;, 'INPCRD': &lt;class 'MDAnalysis.coordinates.INPCRD.INPReader'&gt;, 'PDBQT': &lt;class 'MDAnalysis.coordinates.PDBQT.PDBQTReader'&gt;, 'PQR': &lt;class 'MDAnalysis.coordinates.PQR.PQRReader'&gt;, 'XYZ': &lt;class 'MDAnalysis.coordinates.XYZ.XYZReader'&gt;, 'RESTRT': &lt;class 'MDAnalysis.coordinates.INPCRD.INPReader'&gt;, 'CONFIG': &lt;class 'MDAnalysis.coordinates.DLPoly.ConfigReader'&gt;, 'MOL2': &lt;class 'MDAnalysis.coordinates.MOL2.MOL2Reader'&gt;, 'NCDF': &lt;class 'MDAnalysis.coordinates.TRJ.NCDFReader'&gt;}</em><a class="headerlink" href="#MDAnalysis.coordinates.__init__._trajectory_readers" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.__init__.</code><code class="descname">_trajectory_readers</code><em class="property"> = {'DMS': &lt;class 'MDAnalysis.coordinates.DMS.DMSReader'&gt;, 'CRD': &lt;class 'MDAnalysis.coordinates.CRD.CRDReader'&gt;, 'DATA': &lt;class 'MDAnalysis.coordinates.LAMMPS.DATAReader'&gt;, 'XPDB': &lt;class 'MDAnalysis.coordinates.PDB.ExtendedPDBReader'&gt;, 'CHAIN': &lt;class 'MDAnalysis.coordinates.base.ChainReader'&gt;, 'DCD': &lt;class 'MDAnalysis.coordinates.DCD.DCDReader'&gt;, 'NC': &lt;class 'MDAnalysis.coordinates.TRJ.NCDFReader'&gt;, 'TRJ': &lt;class 'MDAnalysis.coordinates.TRJ.TRJReader'&gt;, 'MDCRD': &lt;class 'MDAnalysis.coordinates.TRJ.TRJReader'&gt;, 'TRZ': &lt;class 'MDAnalysis.coordinates.TRZ.TRZReader'&gt;, 'XTC': &lt;class 'MDAnalysis.coordinates.xdrfile.XTC.XTCReader'&gt;, 'GMS': &lt;class 'MDAnalysis.coordinates.GMS.GMSReader'&gt;, 'GRO': &lt;class 'MDAnalysis.coordinates.GRO.GROReader'&gt;, 'TRR': &lt;class 'MDAnalysis.coordinates.xdrfile.TRR.TRRReader'&gt;, 'PDB': &lt;class 'MDAnalysis.coordinates.PDB.PDBReader'&gt;, 'HISTORY': &lt;class 'MDAnalysis.coordinates.DLPoly.HistoryReader'&gt;, 'LAMMPS': &lt;class 'MDAnalysis.coordinates.LAMMPS.DCDReader'&gt;, 'Permissive_PDB': &lt;class 'MDAnalysis.coordinates.PDB.PrimitivePDBReader'&gt;, 'INPCRD': &lt;class 'MDAnalysis.coordinates.INPCRD.INPReader'&gt;, 'PDBQT': &lt;class 'MDAnalysis.coordinates.PDBQT.PDBQTReader'&gt;, 'PQR': &lt;class 'MDAnalysis.coordinates.PQR.PQRReader'&gt;, 'XYZ': &lt;class 'MDAnalysis.coordinates.XYZ.XYZReader'&gt;, 'RESTRT': &lt;class 'MDAnalysis.coordinates.INPCRD.INPReader'&gt;, 'CONFIG': &lt;class 'MDAnalysis.coordinates.DLPoly.ConfigReader'&gt;, 'MOL2': &lt;class 'MDAnalysis.coordinates.MOL2.MOL2Reader'&gt;, 'NCDF': &lt;class 'MDAnalysis.coordinates.TRJ.NCDFReader'&gt;}</em><a class="headerlink" href="#MDAnalysis.coordinates.__init__._trajectory_readers" title="Permalink to this definition">¶</a></dt>
 <dd><p>standard trajectory readers (dict with identifier as key and reader class as value)</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.__init__._topology_coordinates_readers">
-<tt class="descclassname">MDAnalysis.coordinates.__init__.</tt><tt class="descname">_topology_coordinates_readers</tt><em class="property"> = {'DMS': &lt;class 'MDAnalysis.coordinates.DMS.DMSReader'&gt;, 'CRD': &lt;class 'MDAnalysis.coordinates.CRD.CRDReader'&gt;, 'GMS': &lt;class 'MDAnalysis.coordinates.GMS.GMSReader'&gt;, 'GRO': &lt;class 'MDAnalysis.coordinates.GRO.GROReader'&gt;, 'DATA': &lt;class 'MDAnalysis.coordinates.LAMMPS.DATAReader'&gt;, 'PDB': &lt;class 'MDAnalysis.coordinates.PDB.PrimitivePDBReader'&gt;, 'HISTORY': &lt;class 'MDAnalysis.coordinates.DLPoly.HistoryReader'&gt;, 'XPDB': &lt;class 'MDAnalysis.coordinates.PDB.ExtendedPDBReader'&gt;, 'MOL2': &lt;class 'MDAnalysis.coordinates.MOL2.MOL2Reader'&gt;, 'PDBQT': &lt;class 'MDAnalysis.coordinates.PDBQT.PDBQTReader'&gt;, 'PQR': &lt;class 'MDAnalysis.coordinates.PQR.PQRReader'&gt;, 'CONFIG': &lt;class 'MDAnalysis.coordinates.DLPoly.ConfigReader'&gt;, 'XYZ': &lt;class 'MDAnalysis.coordinates.XYZ.XYZReader'&gt;}</em><a class="headerlink" href="#MDAnalysis.coordinates.__init__._topology_coordinates_readers" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.__init__.</code><code class="descname">_topology_coordinates_readers</code><em class="property"> = {'DMS': &lt;class 'MDAnalysis.coordinates.DMS.DMSReader'&gt;, 'CRD': &lt;class 'MDAnalysis.coordinates.CRD.CRDReader'&gt;, 'GMS': &lt;class 'MDAnalysis.coordinates.GMS.GMSReader'&gt;, 'GRO': &lt;class 'MDAnalysis.coordinates.GRO.GROReader'&gt;, 'DATA': &lt;class 'MDAnalysis.coordinates.LAMMPS.DATAReader'&gt;, 'PDB': &lt;class 'MDAnalysis.coordinates.PDB.PrimitivePDBReader'&gt;, 'HISTORY': &lt;class 'MDAnalysis.coordinates.DLPoly.HistoryReader'&gt;, 'XPDB': &lt;class 'MDAnalysis.coordinates.PDB.ExtendedPDBReader'&gt;, 'MOL2': &lt;class 'MDAnalysis.coordinates.MOL2.MOL2Reader'&gt;, 'PDBQT': &lt;class 'MDAnalysis.coordinates.PDBQT.PDBQTReader'&gt;, 'PQR': &lt;class 'MDAnalysis.coordinates.PQR.PQRReader'&gt;, 'CONFIG': &lt;class 'MDAnalysis.coordinates.DLPoly.ConfigReader'&gt;, 'XYZ': &lt;class 'MDAnalysis.coordinates.XYZ.XYZReader'&gt;}</em><a class="headerlink" href="#MDAnalysis.coordinates.__init__._topology_coordinates_readers" title="Permalink to this definition">¶</a></dt>
 <dd><p>readers of files that contain both topology/atom data and coordinates
 (currently only the keys are used)</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.__init__._compressed_formats">
-<tt class="descclassname">MDAnalysis.coordinates.__init__.</tt><tt class="descname">_compressed_formats</tt><em class="property"> = ['XYZ', 'TRJ', 'MDCRD', 'PQR', 'PDBQT']</em><a class="headerlink" href="#MDAnalysis.coordinates.__init__._compressed_formats" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.__init__.</code><code class="descname">_compressed_formats</code><em class="property"> = ['XYZ', 'TRJ', 'MDCRD', 'PQR', 'PDBQT']</em><a class="headerlink" href="#MDAnalysis.coordinates.__init__._compressed_formats" title="Permalink to this definition">¶</a></dt>
 <dd><p>formats of readers that can also handle gzip or bzip2 compressed files</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.__init__._frame_writers">
-<tt class="descclassname">MDAnalysis.coordinates.__init__.</tt><tt class="descname">_frame_writers</tt><em class="property"> = {'XYZ': &lt;class 'MDAnalysis.coordinates.XYZ.XYZWriter'&gt;, 'PDBQT': &lt;class 'MDAnalysis.coordinates.PDBQT.PDBQTWriter'&gt;, 'MOL2': &lt;class 'MDAnalysis.coordinates.MOL2.MOL2Writer'&gt;, 'PQR': &lt;class 'MDAnalysis.coordinates.PQR.PQRWriter'&gt;, 'CRD': &lt;class 'MDAnalysis.coordinates.CRD.CRDWriter'&gt;, 'GRO': &lt;class 'MDAnalysis.coordinates.GRO.GROWriter'&gt;, 'PDB': &lt;class 'MDAnalysis.coordinates.PDB.PrimitivePDBWriter'&gt;}</em><a class="headerlink" href="#MDAnalysis.coordinates.__init__._frame_writers" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.__init__.</code><code class="descname">_frame_writers</code><em class="property"> = {'XYZ': &lt;class 'MDAnalysis.coordinates.XYZ.XYZWriter'&gt;, 'PDBQT': &lt;class 'MDAnalysis.coordinates.PDBQT.PDBQTWriter'&gt;, 'MOL2': &lt;class 'MDAnalysis.coordinates.MOL2.MOL2Writer'&gt;, 'PQR': &lt;class 'MDAnalysis.coordinates.PQR.PQRWriter'&gt;, 'CRD': &lt;class 'MDAnalysis.coordinates.CRD.CRDWriter'&gt;, 'GRO': &lt;class 'MDAnalysis.coordinates.GRO.GROWriter'&gt;, 'PDB': &lt;class 'MDAnalysis.coordinates.PDB.PrimitivePDBWriter'&gt;}</em><a class="headerlink" href="#MDAnalysis.coordinates.__init__._frame_writers" title="Permalink to this definition">¶</a></dt>
 <dd><p>frame writers: export to single frame formats such as PDB, gro, crd
 Signature:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">W</span> <span class="o">=</span> <span class="n">FrameWriter</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
@@ -874,7 +874,7 @@ <h2>5.1.6. Reader/Writer registry<a class="headerlink" href="#reader-writer-regi
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.__init__._trajectory_writers">
-<tt class="descclassname">MDAnalysis.coordinates.__init__.</tt><tt class="descname">_trajectory_writers</tt><em class="property"> = {'MOL2': &lt;class 'MDAnalysis.coordinates.MOL2.MOL2Writer'&gt;, 'TRZ': &lt;class 'MDAnalysis.coordinates.TRZ.TRZWriter'&gt;, 'XTC': &lt;class 'MDAnalysis.coordinates.xdrfile.XTC.XTCWriter'&gt;, 'XYZ': &lt;class 'MDAnalysis.coordinates.XYZ.XYZWriter'&gt;, 'LAMMPS': &lt;class 'MDAnalysis.coordinates.LAMMPS.DCDWriter'&gt;, 'DCD': &lt;class 'MDAnalysis.coordinates.DCD.DCDWriter'&gt;, 'TRR': &lt;class 'MDAnalysis.coordinates.xdrfile.TRR.TRRWriter'&gt;, 'PDB': &lt;class 'MDAnalysis.coordinates.PDB.MultiPDBWriter'&gt;, 'NCDF': &lt;class 'MDAnalysis.coordinates.TRJ.NCDFWriter'&gt;}</em><a class="headerlink" href="#MDAnalysis.coordinates.__init__._trajectory_writers" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.__init__.</code><code class="descname">_trajectory_writers</code><em class="property"> = {'MOL2': &lt;class 'MDAnalysis.coordinates.MOL2.MOL2Writer'&gt;, 'TRZ': &lt;class 'MDAnalysis.coordinates.TRZ.TRZWriter'&gt;, 'XTC': &lt;class 'MDAnalysis.coordinates.xdrfile.XTC.XTCWriter'&gt;, 'XYZ': &lt;class 'MDAnalysis.coordinates.XYZ.XYZWriter'&gt;, 'LAMMPS': &lt;class 'MDAnalysis.coordinates.LAMMPS.DCDWriter'&gt;, 'DCD': &lt;class 'MDAnalysis.coordinates.DCD.DCDWriter'&gt;, 'TRR': &lt;class 'MDAnalysis.coordinates.xdrfile.TRR.TRRWriter'&gt;, 'PDB': &lt;class 'MDAnalysis.coordinates.PDB.MultiPDBWriter'&gt;, 'NCDF': &lt;class 'MDAnalysis.coordinates.TRJ.NCDFWriter'&gt;}</em><a class="headerlink" href="#MDAnalysis.coordinates.__init__._trajectory_writers" title="Permalink to this definition">¶</a></dt>
 <dd><p>trajectory writers: export frames, typically only saving coordinates
 Signature:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">W</span> <span class="o">=</span> <span class="n">TrajectoryWriter</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="n">n_atoms</span><span class="p">,</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
@@ -895,7 +895,7 @@ <h2>5.1.6. Reader/Writer registry<a class="headerlink" href="#reader-writer-regi
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -910,11 +910,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../coordinates_modules.html" title="5. Coordinates modules"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -924,7 +924,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/pdbextensions.html b/package/doc/html/documentation_pages/coordinates/pdbextensions.html
index 4ec8313ba38..0d0c0acc4ff 100644
--- a/package/doc/html/documentation_pages/coordinates/pdbextensions.html
+++ b/package/doc/html/documentation_pages/coordinates/pdbextensions.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.22. Extensions to Bio.PDB — pdb.extensions &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.22. Extensions to Bio.PDB — pdb.extensions &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="6. Selection exporters" href="../selections_modules.html" />
     <link rel="prev" title="5.21.5. Status codes and symbols — statno" href="xdrfile/statno.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="xdrfile/statno.html" title="5.21.5. Status codes and symbols — statno"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.22. Extensions to <tt class="docutils literal"><span class="pre">Bio.PDB</span></tt> &#8212; <tt class="docutils literal"><span class="pre">pdb.extensions</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.22. Extensions to <code class="docutils literal"><span class="pre">Bio.PDB</span></code> &#8212; <code class="docutils literal"><span class="pre">pdb.extensions</span></code></a><ul>
 <li><a class="reference internal" href="#classes">5.22.1. Classes</a></li>
 <li><a class="reference internal" href="#functions">5.22.2. Functions</a></li>
 </ul>
@@ -71,16 +69,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="xdrfile/statno.html"
-                        title="previous chapter">5.21.5. Status codes and symbols &#8212; <tt class="docutils literal"><span class="pre">statno</span></tt></a></p>
+                        title="previous chapter">5.21.5. Status codes and symbols &#8212; <code class="docutils literal"><span class="pre">statno</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="../selections_modules.html"
                         title="next chapter">6. Selection exporters</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/pdbextensions.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/pdbextensions.txt"
+            rel="nofollow">Show Source</a></li>
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+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -99,10 +99,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.pdb.extensions"></span><div class="section" id="extensions-to-bio-pdb-pdb-extensions">
-<h1>5.22. Extensions to <tt class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></tt> &#8212; <tt class="xref py py-mod docutils literal"><span class="pre">pdb.extensions</span></tt><a class="headerlink" href="#extensions-to-bio-pdb-pdb-extensions" title="Permalink to this headline">¶</a></h1>
+<h1>5.22. Extensions to <code class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></code> &#8212; <code class="xref py py-mod docutils literal"><span class="pre">pdb.extensions</span></code><a class="headerlink" href="#extensions-to-bio-pdb-pdb-extensions" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -115,7 +115,7 @@ <h1>5.22. Extensions to <tt class="xref py py-mod docutils literal"><span class=
 </tr>
 </tbody>
 </table>
-<p>Extension to <tt class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></tt> to handle large pdb files.</p>
+<p>Extension to <code class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></code> to handle large pdb files.</p>
 <p>Partly published on <a class="reference external" href="http://biopython.org/wiki/Reading_large_PDB_files">http://biopython.org/wiki/Reading_large_PDB_files</a>
 and more code at
 <a class="reference external" href="http://github.com/orbeckst/GromacsWrapper/tree/master/edPDB/">http://github.com/orbeckst/GromacsWrapper/tree/master/edPDB/</a></p>
@@ -123,9 +123,9 @@ <h1>5.22. Extensions to <tt class="xref py py-mod docutils literal"><span class=
 <h2>5.22.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.pdb.extensions.SloppyStructureBuilder">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.pdb.extensions.</tt><tt class="descname">SloppyStructureBuilder</tt><big>(</big><em>verbose=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/pdb/extensions.html#SloppyStructureBuilder"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.pdb.extensions.SloppyStructureBuilder" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.pdb.extensions.</code><code class="descname">SloppyStructureBuilder</code><span class="sig-paren">(</span><em>verbose=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/pdb/extensions.html#SloppyStructureBuilder"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.pdb.extensions.SloppyStructureBuilder" title="Permalink to this definition">¶</a></dt>
 <dd><p>Cope with resSeq &lt; 10,000 limitation by just incrementing internally.</p>
-<p>Solves the follwing problem with <tt class="xref py py-class docutils literal"><span class="pre">Bio.PDB.StructureBuilder.StructureBuilder</span></tt>:</p>
+<p>Solves the follwing problem with <code class="xref py py-class docutils literal"><span class="pre">Bio.PDB.StructureBuilder.StructureBuilder</span></code>:</p>
 <dl class="docutils">
 <dt>Q: What&#8217;s wrong here??</dt>
 <dd>Some atoms or residues will be missing in the data structure.
@@ -141,7 +141,7 @@ <h2>5.22.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.pdb.extensions.SloppyPDBIO">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.pdb.extensions.</tt><tt class="descname">SloppyPDBIO</tt><big>(</big><em>use_model_flag=0</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/pdb/extensions.html#SloppyPDBIO"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.pdb.extensions.SloppyPDBIO" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.pdb.extensions.</code><code class="descname">SloppyPDBIO</code><span class="sig-paren">(</span><em>use_model_flag=0</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/pdb/extensions.html#SloppyPDBIO"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.pdb.extensions.SloppyPDBIO" title="Permalink to this definition">¶</a></dt>
 <dd><p>PDBIO class that can deal with large pdb files as used in MD simulations.</p>
 <ul class="simple">
 <li>resSeq simply wrap and are printed modulo 10,000.</li>
@@ -157,26 +157,26 @@ <h2>5.22.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 <h2>5.22.2. Functions<a class="headerlink" href="#functions" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.coordinates.pdb.extensions.get_structure">
-<tt class="descclassname">MDAnalysis.coordinates.pdb.extensions.</tt><tt class="descname">get_structure</tt><big>(</big><em>pdbfile</em>, <em>pdbid='system'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/pdb/extensions.html#get_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.pdb.extensions.get_structure" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.pdb.extensions.</code><code class="descname">get_structure</code><span class="sig-paren">(</span><em>pdbfile</em>, <em>pdbid='system'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/pdb/extensions.html#get_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.pdb.extensions.get_structure" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the <em>pdbfilename</em>  and return a Bio.PDB structure.</p>
 <p>This function ignores duplicate atom numbers and resids from the
 file and simply increments them.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The call signature is reversed compared to the one of
-<tt class="xref py py-meth docutils literal"><span class="pre">Bio.PDB.PDBParser.get_structure()</span></tt>.</p>
+<code class="xref py py-meth docutils literal"><span class="pre">Bio.PDB.PDBParser.get_structure()</span></code>.</p>
 </div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.coordinates.pdb.extensions.write_pdb">
-<tt class="descclassname">MDAnalysis.coordinates.pdb.extensions.</tt><tt class="descname">write_pdb</tt><big>(</big><em>structure</em>, <em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/pdb/extensions.html#write_pdb"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.pdb.extensions.write_pdb" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.pdb.extensions.</code><code class="descname">write_pdb</code><span class="sig-paren">(</span><em>structure</em>, <em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/pdb/extensions.html#write_pdb"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.pdb.extensions.write_pdb" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write Bio.PDB molecule <em>structure</em> to <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>structure</em></dt>
 <dd><p class="first last">Bio.PDB structure instance</p>
 </dd>
@@ -202,7 +202,7 @@ <h2>5.22.2. Functions<a class="headerlink" href="#functions" title="Permalink to
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -217,11 +217,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="xdrfile/statno.html" title="5.21.5. Status codes and symbols — statno"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -231,7 +231,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile.html b/package/doc/html/documentation_pages/coordinates/xdrfile.html
index 2519e4162be..38a1d2fa8f9 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.21. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.21. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="next" title="5.21.1. Gromacs XTC trajectory I/O — MDAnalysis.coordinates.xdrfile.XTC" href="xdrfile/XTC.html" />
     <link rel="prev" title="5.20. Common functions for coordinate reading — MDAnalysis.coordinates.core" href="core.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
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@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="core.html" title="5.20. Common functions for coordinate reading — MDAnalysis.coordinates.core"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" accesskey="U">5. Coordinates modules</a> &raquo;</li> 
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="core.html"
-                        title="previous chapter">5.20. Common functions for coordinate reading &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.core</span></tt></a></p>
+                        title="previous chapter">5.20. Common functions for coordinate reading &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.core</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="xdrfile/XTC.html"
-                        title="next chapter">5.21.1. Gromacs XTC trajectory I/O &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.XTC</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/coordinates/xdrfile.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.21.1. Gromacs XTC trajectory I/O &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.XTC</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/coordinates/xdrfile.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,28 +90,28 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="numpy-access-to-gromacs-xdr-trajectories-mdanalysis-coordinates-xdrfile">
-<h1>5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt><a class="headerlink" href="#numpy-access-to-gromacs-xdr-trajectories-mdanalysis-coordinates-xdrfile" title="Permalink to this headline">¶</a></h1>
+<h1>5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code><a class="headerlink" href="#numpy-access-to-gromacs-xdr-trajectories-mdanalysis-coordinates-xdrfile" title="Permalink to this headline">¶</a></h1>
 <p><a class="reference external" href="http://www.gromacs.org">Gromacs</a> trajectory formats are based on the <a class="reference external" href="http://en.wikipedia.org/wiki/External_Data_Representation">XDR</a> (eXternal Data
 Representation) format. Within this module, classes are provided to
-access frames of Gromacs <a class="reference internal" href="XTC.html#module-MDAnalysis.coordinates.XTC" title="MDAnalysis.coordinates.XTC"><tt class="xref py py-mod docutils literal"><span class="pre">XTC</span></tt></a> or
-<a class="reference internal" href="TRR.html#module-MDAnalysis.coordinates.TRR" title="MDAnalysis.coordinates.TRR"><tt class="xref py py-mod docutils literal"><span class="pre">TRR</span></tt></a> trajectories. Relevant data
+access frames of Gromacs <a class="reference internal" href="XTC.html#module-MDAnalysis.coordinates.XTC" title="MDAnalysis.coordinates.XTC"><code class="xref py py-mod docutils literal"><span class="pre">XTC</span></code></a> or
+<a class="reference internal" href="TRR.html#module-MDAnalysis.coordinates.TRR" title="MDAnalysis.coordinates.TRR"><code class="xref py py-mod docutils literal"><span class="pre">TRR</span></code></a> trajectories. Relevant data
 (positions, velocities, forces, box dimensions) are made available as
 <a class="reference external" href="http://www.numpy.org/">NumPy</a> arrays. The module also contains low-level code in
-<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt></a> that performs the
+<a class="reference internal" href="xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code></a> that performs the
 actual file access and includes some additions such as trajectory
 indices that provide random access for the Gromacs trajectories (which
 is not available with current standard Gromacs tools).</p>
 <p class="rubric">Contents</p>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="xdrfile/XTC.html">5.21.1. Gromacs XTC trajectory I/O &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.XTC</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="xdrfile/TRR.html">5.21.2. Gromacs TRR trajectory I/O &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.TRR</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="xdrfile/core.html">5.21.3. Common high-level Gromacs XDR functionality &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.core</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="xdrfile/libxdrfile2.html">5.21.4. The Gromacs XTC/TRR library <tt class="docutils literal"><span class="pre">libxdrfile2</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="xdrfile/statno.html">5.21.5. Status codes and symbols &#8212; <tt class="docutils literal"><span class="pre">statno</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="xdrfile/XTC.html">5.21.1. Gromacs XTC trajectory I/O &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.XTC</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="xdrfile/TRR.html">5.21.2. Gromacs TRR trajectory I/O &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.TRR</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="xdrfile/core.html">5.21.3. Common high-level Gromacs XDR functionality &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.core</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="xdrfile/libxdrfile2.html">5.21.4. The Gromacs XTC/TRR library <code class="docutils literal"><span class="pre">libxdrfile2</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="xdrfile/statno.html">5.21.5. Status codes and symbols &#8212; <code class="docutils literal"><span class="pre">statno</span></code></a></li>
 </ul>
 </div>
 </div>
@@ -122,7 +122,7 @@ <h1>5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="xref py py
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
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@@ -137,11 +137,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="core.html" title="5.20. Common functions for coordinate reading — MDAnalysis.coordinates.core"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li> 
       </ul>
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-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -151,7 +151,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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   </body>
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\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile/TRR.html b/package/doc/html/documentation_pages/coordinates/xdrfile/TRR.html
index b6131ecb2fc..255556c02db 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile/TRR.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile/TRR.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.21.2. Gromacs TRR trajectory I/O — MDAnalysis.coordinates.xdrfile.TRR &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.21.2. Gromacs TRR trajectory I/O — MDAnalysis.coordinates.xdrfile.TRR &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
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         HAS_SOURCE:  true
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-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
     <link rel="up" title="5.21. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile" href="../xdrfile.html" />
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     <link rel="prev" title="5.21.1. Gromacs XTC trajectory I/O — MDAnalysis.coordinates.xdrfile.XTC" href="XTC.html" /> 
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+    <div class="related" role="navigation" aria-label="related navigation">
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           <a href="XTC.html" title="5.21.1. Gromacs XTC trajectory I/O — MDAnalysis.coordinates.xdrfile.XTC"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
-          <li><a href="../xdrfile.html" accesskey="U">5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
+          <li class="nav-item nav-item-2"><a href="../xdrfile.html" accesskey="U">5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a> &raquo;</li> 
       </ul>
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.21.2. Gromacs TRR trajectory I/O &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.TRR</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.21.2. Gromacs TRR trajectory I/O &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.TRR</span></code></a><ul>
 <li><a class="reference internal" href="#classes">5.21.2.1. Classes</a></li>
 </ul>
 </li>
@@ -71,16 +69,18 @@ <h3><a href="../../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="XTC.html"
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+                        title="previous chapter">5.21.1. Gromacs XTC trajectory I/O &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.XTC</span></code></a></p>
   <h4>Next topic</h4>
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-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../../_sources/documentation_pages/coordinates/xdrfile/TRR.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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+                        title="next chapter">5.21.3. Common high-level Gromacs XDR functionality &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.core</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
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+            rel="nofollow">Show Source</a></li>
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   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
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   <span class="target" id="module-MDAnalysis.coordinates.xdrfile.TRR"></span><div class="section" id="gromacs-trr-trajectory-i-o-mdanalysis-coordinates-xdrfile-trr">
-<h1>5.21.2. Gromacs TRR trajectory I/O &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.xdrfile.TRR" title="MDAnalysis.coordinates.xdrfile.TRR"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.TRR</span></tt></a><a class="headerlink" href="#gromacs-trr-trajectory-i-o-mdanalysis-coordinates-xdrfile-trr" title="Permalink to this headline">¶</a></h1>
+<h1>5.21.2. Gromacs TRR trajectory I/O &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.xdrfile.TRR" title="MDAnalysis.coordinates.xdrfile.TRR"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.TRR</span></code></a><a class="headerlink" href="#gromacs-trr-trajectory-i-o-mdanalysis-coordinates-xdrfile-trr" title="Permalink to this headline">¶</a></h1>
 <p>Classes for reading and writing of <a class="reference external" href="http://www.gromacs.org/Documentation/File_Formats/.trr_File">Gromacs TRR trajectories</a>
 together with supporting code.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">Users should access classes from <a class="reference internal" href="../TRR.html#module-MDAnalysis.coordinates.TRR" title="MDAnalysis.coordinates.TRR"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRR</span></tt></a>.</p>
+<p class="last">Users should access classes from <a class="reference internal" href="../TRR.html#module-MDAnalysis.coordinates.TRR" title="MDAnalysis.coordinates.TRR"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.TRR</span></code></a>.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.libxdrfile2</span></tt></a> for low-level
+<p class="last"><a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.libxdrfile2</span></code></a> for low-level
 bindings to the Gromacs trajectory file formats</p>
 </div>
 <div class="section" id="classes">
 <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.Timestep">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.xdrfile.TRR.</tt><tt class="descname">Timestep</tt><big>(</big><em>n_atoms</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/TRR.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.xdrfile.TRR.</code><code class="descname">Timestep</code><span class="sig-paren">(</span><em>n_atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/TRR.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Timestep for a <a class="reference external" href="http://www.gromacs.org">Gromacs</a> TRR trajectory.</p>
 <p>TRR Timestep always has positions, velocities and forces allocated, meaning
 that the <cite>_pos</cite>, <cite>_velocities</cite> and <cite>_forces</cite> attributes will always exist.
@@ -127,9 +127,9 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 by the entries in the data dictionary: <cite>position_source</cite>, <cite>velocity_source</cite>
 and <cite>force_source</cite>.
 When accessing the <cite>.positions</cite> attribute, this will only be returned if
-<cite>position_source</cite> matches the current <cite>frame</cite>, otherwise a <tt class="xref py py-class docutils literal"><span class="pre">NoDataError</span></tt>
+<cite>position_source</cite> matches the current <cite>frame</cite>, otherwise a <code class="xref py py-class docutils literal"><span class="pre">NoDataError</span></code>
 will be raised.  This scheme applies to both velocities and forces.</p>
-<p>When writing to the Timestep, it is important that the <tt class="xref py py-attr docutils literal"><span class="pre">frame</span></tt>
+<p>When writing to the Timestep, it is important that the <code class="xref py py-attr docutils literal"><span class="pre">frame</span></code>
 attribute is updated first!  This is because the source of the data is
 taken as the current frame of the Timestep.</p>
 <p>For example:</p>
@@ -148,34 +148,36 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
               <span class="c"># velocities was populated</span>
 </pre></div>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span>TRR <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects are now fully aware of the existence or
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span>TRR <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects are now fully aware of the existence or
 not of coordinate/velocity/force information in frames.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Velocities and forces can now be directly accessed via the <cite>velocities</cite> and
-<cite>forces</cite> attributes, with a <tt class="xref py py-class docutils literal"><span class="pre">NoDataError</span></tt> being raised
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Velocities and forces can now be directly accessed via the <cite>velocities</cite> and
+<cite>forces</cite> attributes, with a <code class="xref py py-class docutils literal"><span class="pre">NoDataError</span></code> being raised
 if no data was given for that frame.
 Management redone to use <cite>has_positions</cite>, <cite>has_velocities</cite> and
 <cite>has_forces</cite>.  Setting these will update the data dictionary entries
 which track the data.
 Timestep lmbda now stored in the data dictionary </p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.Timestep.copy">
-<tt class="descname">copy</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.copy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>.</p>
+<code class="descname">copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.Timestep.copy_slice">
-<tt class="descname">copy_slice</tt><big>(</big><em>sel</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
+<code class="descname">copy_slice</code><span class="sig-paren">(</span><em>sel</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy_slice"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
 <dd><p>Make a new Timestep containing a subset of the original Timestep.</p>
-<p><tt class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></tt>
-<tt class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></tt></p>
+<p><code class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></code>
+<code class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></code></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A Timestep object of the same type containing all header
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A Timestep object of the same type containing all header
 information and all atom information relevant to the selection.</td>
 </tr>
 </tbody>
@@ -185,16 +187,18 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <p class="last">The selection must be a 0 based slice or array of the atom indices
 in this Timestep</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
 copy official attributes of the Timestep.</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.Timestep.dimensions">
-<tt class="descname">dimensions</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>unitcell dimensions (A, B, C, alpha, beta, gamma)</p>
 <ul class="simple">
 <li>A, B, C are the lengths of the primitive cell vectors e1, e2, e3</li>
@@ -206,43 +210,47 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.Timestep.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.dt" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dt</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.dt" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time difference in ps between timesteps</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">This defaults to 1.0 ps in the absence of time data</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
-<dl class="classmethod">
+<dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.Timestep.from_coordinates">
-<em class="property">classmethod </em><tt class="descname">from_coordinates</tt><big>(</big><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
+<code class="descname">from_coordinates</code><span class="sig-paren">(</span><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_coordinates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create an instance of this Timestep, from coordinate data</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
-<dl class="classmethod">
+<dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.Timestep.from_timestep">
-<em class="property">classmethod </em><tt class="descname">from_timestep</tt><big>(</big><em>other</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">from_timestep</code><span class="sig-paren">(</span><em>other</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a copy of another Timestep, in the format of this Timestep</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.Timestep.n_atoms">
-<tt class="descname">n_atoms</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>A read only view of the number of atoms this Timestep has</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.Timestep.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time in ps of this timestep</p>
 <p>This is calculated as:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">time</span>
@@ -252,19 +260,20 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span> <span class="o">*</span> <span class="n">ts</span><span class="o">.</span><span class="n">dt</span>
 </pre></div>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.Timestep.triclinic_dimensions">
-<tt class="descname">triclinic_dimensions</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">triclinic_dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>The unitcell dimensions represented as triclinic vectors</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
 </tr>
 </tbody>
 </table>
@@ -284,17 +293,18 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <span class="go">        72.45159912,  71.56504822], dtype=float32)</span>
 </pre></div>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="../../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.Timestep.volume">
-<tt class="descname">volume</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.volume" title="Permalink to this definition">¶</a></dt>
+<code class="descname">volume</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.volume" title="Permalink to this definition">¶</a></dt>
 <dd><p>volume of the unitcell</p>
 </dd></dl>
 
@@ -302,29 +312,31 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.xdrfile.TRR.</tt><tt class="descname">TRRReader</tt><big>(</big><em>filename</em>, <em>sub=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/TRR.html#TRRReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.xdrfile.TRR.</code><code class="descname">TRRReader</code><span class="sig-paren">(</span><em>filename</em>, <em>sub=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/TRR.html#TRRReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read a <a class="reference external" href="http://www.gromacs.org">Gromacs</a> TRR trajectory.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span><a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects returned from TRR files now have
-<tt class="xref py py-attr docutils literal"><span class="pre">has_x</span></tt>, <tt class="xref py py-attr docutils literal"><span class="pre">has_velocities</span></tt>, and <tt class="xref py py-attr docutils literal"><span class="pre">has_forces</span></tt>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span><a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects returned from TRR files now have
+<code class="xref py py-attr docutils literal"><span class="pre">has_x</span></code>, <code class="xref py py-attr docutils literal"><span class="pre">has_velocities</span></code>, and <code class="xref py py-attr docutils literal"><span class="pre">has_forces</span></code>
 flags reflecting whether coordinates/velocities/forces were read.
-Attempting to access such data when the corresponding flag is set to <tt class="docutils literal"><span class="pre">False</span></tt>
-will raise a <tt class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></tt>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Returned Timesteps will always be a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance.
+Attempting to access such data when the corresponding flag is set to <code class="docutils literal"><span class="pre">False</span></code>
+will raise a <code class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></code>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Returned Timesteps will always be a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance.
 Attributes lmbda and status now stored in the TS.data dictionary</p>
+</div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">the name of the trr file.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>sub</em></dt>
 <dd><p class="first">an numpy integer array of what subset of trajectory atoms to load into
 the timestep. Intended to work similarly to the &#8216;sub&#8217; argument to <a class="reference external" href="http://www.gromacs.org">Gromacs</a>&#8216; trjconv.</p>
@@ -334,47 +346,50 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 equal to number of atoms in the Universe.</p>
 </dd>
 <dt><em>refresh_offsets</em></dt>
-<dd><p class="first last">if <tt class="docutils literal"><span class="pre">True</span></tt>, do not retrieve stored offsets, but instead generate
-new ones; if <tt class="docutils literal"><span class="pre">False</span></tt>, use retrieved offsets if available [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">if <code class="docutils literal"><span class="pre">True</span></code>, do not retrieve stored offsets, but instead generate
+new ones; if <code class="docutils literal"><span class="pre">False</span></code>, use retrieved offsets if available [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>refresh_offsets</em></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Renamed &#8220;delta&#8221; attribute to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>refresh_offsets</em></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Renamed &#8220;delta&#8221; attribute to &#8220;dt&#8221;
+Now passes weakref of self to ts (as &#8220;_reader&#8221;)</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.OtherWriter">
-<tt class="descname">OtherWriter</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">OtherWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a writer appropriate for <em>filename</em>.</p>
 <p>Sets the default keywords <em>start</em>, <em>step</em> and <em>dt</em> (if
-available). <em>n_atoms</em> is always set from <tt class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></tt>.</p>
-<div class="admonition-see-also admonition seealso">
+available). <em>n_atoms</em> is always set from <code class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></code>.</p>
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></tt> and <tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></tt></p>
+<p class="last"><code class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></code> and <code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a Gromacs TrjWriter for <em>filename</em> with the same parameters as this trajectory.</p>
 <p>All values can be changed through keyword arguments.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">number of atoms</p>
 </dd>
@@ -388,132 +403,139 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">appropriate <tt class="xref py py-class docutils literal"><span class="pre">TrjWriter</span></tt></p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">appropriate <code class="xref py py-class docutils literal"><span class="pre">TrjWriter</span></code></p>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Changed &#8220;delta&#8221; keyword to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Changed &#8220;delta&#8221; keyword to &#8220;dt&#8221;</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close xdr trajectory file if it was open.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.dt" title="Permalink to this definition">¶</a></dt>
-<dd><p>Time step length in ps.</p>
-<p>The result is computed from the trajectory and cached. If for
-any reason the trajectory cannot be read then 0 is returned.</p>
+<code class="descname">dt</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.dt" title="Permalink to this definition">¶</a></dt>
+<dd><p>Time between two trajectory frames in picoseconds.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.frame">
-<tt class="descname">frame</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.frame" title="Permalink to this definition">¶</a></dt>
+<code class="descname">frame</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.frame" title="Permalink to this definition">¶</a></dt>
 <dd><p>Frame number of the current time step.</p>
-<p>This is a simple short cut to <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt>.</p>
+<p>This is a simple short cut to <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.load_offsets">
-<tt class="descname">load_offsets</tt><big>(</big><em>filename</em>, <em>check=False</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.load_offsets" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_offsets</code><span class="sig-paren">(</span><em>filename</em>, <em>check=False</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.load_offsets" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads current trajectory offsets from pickled <em>filename</em>.</p>
 <p>Checks if ctime and size of trajectory file matches that stored in
-pickled <em>filename</em>.  If either one does not match (and <em>check</em> == <tt class="docutils literal"><span class="pre">True</span></tt>)
+pickled <em>filename</em>.  If either one does not match (and <em>check</em> == <code class="docutils literal"><span class="pre">True</span></code>)
 then the offsets are not loaded.  This is intended to conservatively
 avoid loading out-of-date offsets.</p>
 <dl class="docutils">
@@ -532,22 +554,22 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
-<dd><p class="first last">filename of pickle file saved with <tt class="xref py py-meth docutils literal"><span class="pre">save_offsets()</span></tt> 
+<dd><p class="first last">filename of pickle file saved with <code class="xref py py-meth docutils literal"><span class="pre">save_offsets()</span></code> 
 with the frame offsets for the loaded trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>check</em></dt>
 <dd><p class="first last">if False, ignore ctime and size check of trajectory file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> if the file cannot be read (see <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">open()</span></tt></a>).</p>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> if the file cannot be read (see <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">open()</span></code></a>).</p>
 </td>
 </tr>
 </tbody>
@@ -556,7 +578,7 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.n_atoms">
-<tt class="descname">n_atoms</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>The number of publically available atoms that this reader will store in the timestep.</p>
 <p>If &#8216;sub&#8217; was not given in the ctor, then this value will just be the actual
 number of atoms in the underlying trajectory file. If however &#8216;sub&#8217; was given, then
@@ -566,7 +588,7 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.n_frames">
-<tt class="descname">n_frames</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.n_frames" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_frames</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.n_frames" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the number of frames from the trajectory.</p>
 <p>The result is cached. If for any reason the trajectory cannot
 be read then 0 is returned.</p>
@@ -574,29 +596,29 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 iterating through the whole trajectory. If the trajectory
 was previously loaded and saved offsets exist, then
 loading will be significantly faster.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-meth docutils literal"><span class="pre">TrjReader.load_offsets()</span></tt> and <tt class="xref py py-meth docutils literal"><span class="pre">TrjReader.save_offsets()</span></tt></p>
+<p class="last"><code class="xref py py-meth docutils literal"><span class="pre">TrjReader.load_offsets()</span></code> and <code class="xref py py-meth docutils literal"><span class="pre">TrjReader.save_offsets()</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.next">
-<tt class="descname">next</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.next" title="Permalink to this definition">¶</a></dt>
+<code class="descname">next</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.next" title="Permalink to this definition">¶</a></dt>
 <dd><p>Forward one step to next frame.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.open_trajectory">
-<tt class="descname">open_trajectory</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
+<code class="descname">open_trajectory</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
 <dd><p>Open xdr trajectory file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">pointer to XDRFILE (and sets self.xdrfile)</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">pointer to XDRFILE (and sets self.xdrfile)</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> with code EALREADY if file was already opened or
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> with code EALREADY if file was already opened or
 ENOENT if the file cannot be found</td>
 </tr>
 </tbody>
@@ -605,13 +627,13 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.rewind">
-<tt class="descname">rewind</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.rewind" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rewind</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.rewind" title="Permalink to this definition">¶</a></dt>
 <dd><p>Position at beginning of trajectory</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.save_offsets">
-<tt class="descname">save_offsets</tt><big>(</big><em>filename</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.save_offsets" title="Permalink to this definition">¶</a></dt>
+<code class="descname">save_offsets</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.save_offsets" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves current trajectory offsets into <em>filename</em>, as a pickled object.</p>
 <p>Along with the offsets themselves, the ctime and file size of the
 trajectory file are also saved.  These are used upon load as a check to
@@ -633,7 +655,7 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename in which to save the frame offsets</p>
 </dd>
@@ -646,15 +668,15 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>Time of the current frame in MDAnalysis time units (typically ps).</p>
 <p>This is either read straight from the Timestep, or calculated as
-time = <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt> * <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.dt" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep.dt"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></tt></a></p>
+time = <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code> * <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.dt" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep.dt"><code class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></code></a></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRReader.totaltime">
-<tt class="descname">totaltime</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.totaltime" title="Permalink to this definition">¶</a></dt>
+<code class="descname">totaltime</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.totaltime" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total length of the trajectory n_frames * dt.</p>
 </dd></dl>
 
@@ -662,14 +684,14 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.xdrfile.TRR.</tt><tt class="descname">TRRWriter</tt><big>(</big><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=None</em>, <em>precision=1000.0</em>, <em>remarks=None</em>, <em>convert_units=None</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/TRR.html#TRRWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.xdrfile.TRR.</code><code class="descname">TRRWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=None</em>, <em>precision=1000.0</em>, <em>remarks=None</em>, <em>convert_units=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/TRR.html#TRRWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a <a class="reference external" href="http://www.gromacs.org">Gromacs</a> TRR trajectory.</p>
 <p>Create a new TrjWriter</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of output file</p>
 </dd>
@@ -679,7 +701,7 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>start</em></dt>
 <dd><p class="first last">starting timestep frame; only used when <em>dt</em> is set.</p>
 </dd>
@@ -688,9 +710,9 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </dd>
 <dt><em>dt</em></dt>
 <dd><p class="first last">time between frames to use. If set will override any time information
-contained in the passed <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects, which will otherwise
+contained in the passed <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects, which will otherwise
 be used.
-The <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.time" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep.time"><tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt></a> attribute defaults to a timestep of
+The <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep.time" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep.time"><code class="xref py py-attr docutils literal"><span class="pre">time</span></code></a> attribute defaults to a timestep of
 to setting the trajectory time at 1 ps per step if there is no
 time information.</p>
 </dd>
@@ -699,121 +721,131 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 for TRR) [1000.0]</p>
 </dd>
 <dt><em>convert_units</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: units are converted to the MDAnalysis base format; <tt class="docutils literal"><span class="pre">None</span></tt> selects
-the value of <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> [&#8216;convert_lengths&#8217;].
-(see <a class="reference internal" href="../../core/init.html#flags-label"><em>Flags</em></a>)</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: units are converted to the MDAnalysis base format; <code class="docutils literal"><span class="pre">None</span></code> selects
+the value of <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> [&#8216;convert_lengths&#8217;].
+(see <a class="reference internal" href="../../core/init.html#flags-label"><span>Flags</span></a>)</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span>The TRR writer is now able to write TRRs without coordinates/velocities/forces,
-depending on the properties available in the <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects passed to
-<a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write" title="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Keyword &#8220;delta&#8221; renamed to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span>The TRR writer is now able to write TRRs without coordinates/velocities/forces,
+depending on the properties available in the <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects passed to
+<a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write" title="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Keyword &#8220;delta&#8221; renamed to &#8220;dt&#8221;</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_dimensions_to_unitcell">
-<tt class="descname">convert_dimensions_to_unitcell</tt><big>(</big><em>ts</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_dimensions_to_unitcell</code><span class="sig-paren">(</span><em>ts</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read dimensions from timestep <em>ts</em> and return Gromacs box vectors</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.has_valid_coordinates">
-<tt class="descname">has_valid_coordinates</tt><big>(</big><em>criteria</em>, <em>x</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns <tt class="docutils literal"><span class="pre">True</span></tt> if all values are within limit values of their formats.</p>
+<code class="descname">has_valid_coordinates</code><span class="sig-paren">(</span><em>criteria</em>, <em>x</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns <code class="docutils literal"><span class="pre">True</span></code> if all values are within limit values of their formats.</p>
 <p>Due to rounding, the test is asymmetric (and <em>min</em> is supposed to be negative):</p>
 <blockquote>
 <div>min &lt; x &lt;= max</div></blockquote>
@@ -821,17 +853,17 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>criteria</em></dt>
 <dd><p class="first last">dictionary containing the <em>max</em> and <em>min</em> values in native units</p>
 </dd>
 <dt><em>x</em></dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></tt> of <tt class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></tt> coordinates of atoms selected to be written out.</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></code> of <code class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></code> coordinates of atoms selected to be written out.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">boolean</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">boolean</p>
 </td>
 </tr>
 </tbody>
@@ -840,10 +872,10 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write">
-<tt class="descname">write</tt><big>(</big><em>obj</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write current timestep, using the supplied <em>obj</em>.</p>
-<p>The argument should be a <a class="reference internal" href="../../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> or
-a <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> or a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance.</p>
+<p>The argument should be a <a class="reference internal" href="../../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> or
+a <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> or a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The size of the <em>obj</em> must be the same as the number of atom
@@ -853,9 +885,9 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write_next_timestep">
-<tt class="descname">write_next_timestep</tt><big>(</big><em>ts=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_next_timestep</code><span class="sig-paren">(</span><em>ts=None</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>write a new timestep to the trj file</p>
-<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance containing coordinates to
+<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.TRR.Timestep" title="MDAnalysis.coordinates.xdrfile.TRR.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance containing coordinates to
 be written to trajectory file</p>
 </dd></dl>
 
@@ -870,7 +902,7 @@ <h2>5.21.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -885,12 +917,12 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="XTC.html" title="5.21.1. Gromacs XTC trajectory I/O — MDAnalysis.coordinates.xdrfile.XTC"
              >previous</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
-          <li><a href="../xdrfile.html" >5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
+          <li class="nav-item nav-item-2"><a href="../xdrfile.html" >5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -900,7 +932,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile/XTC.html b/package/doc/html/documentation_pages/coordinates/xdrfile/XTC.html
index c6b525f66f1..c5428293cbf 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile/XTC.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile/XTC.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.21.1. Gromacs XTC trajectory I/O — MDAnalysis.coordinates.xdrfile.XTC &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.21.1. Gromacs XTC trajectory I/O — MDAnalysis.coordinates.xdrfile.XTC &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
     <link rel="up" title="5.21. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile" href="../xdrfile.html" />
     <link rel="next" title="5.21.2. Gromacs TRR trajectory I/O — MDAnalysis.coordinates.xdrfile.TRR" href="TRR.html" />
     <link rel="prev" title="5.21. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile" href="../xdrfile.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,19 +49,19 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../xdrfile.html" title="5.21. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
-          <li><a href="../xdrfile.html" accesskey="U">5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal docutils literal docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
+          <li class="nav-item nav-item-2"><a href="../xdrfile.html" accesskey="U">5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.21.1. Gromacs XTC trajectory I/O &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.XTC</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.21.1. Gromacs XTC trajectory I/O &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.XTC</span></code></a><ul>
 <li><a class="reference internal" href="#classes">5.21.1.1. Classes</a></li>
 </ul>
 </li>
@@ -71,16 +69,18 @@ <h3><a href="../../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="../xdrfile.html"
-                        title="previous chapter">5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a></p>
+                        title="previous chapter">5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="TRR.html"
-                        title="next chapter">5.21.2. Gromacs TRR trajectory I/O &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.TRR</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../../_sources/documentation_pages/coordinates/xdrfile/XTC.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.21.2. Gromacs TRR trajectory I/O &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.TRR</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../../_sources/documentation_pages/coordinates/xdrfile/XTC.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -99,47 +99,48 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.xdrfile.XTC"></span><div class="section" id="gromacs-xtc-trajectory-i-o-mdanalysis-coordinates-xdrfile-xtc">
-<h1>5.21.1. Gromacs XTC trajectory I/O &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.xdrfile.XTC" title="MDAnalysis.coordinates.xdrfile.XTC"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.XTC</span></tt></a><a class="headerlink" href="#gromacs-xtc-trajectory-i-o-mdanalysis-coordinates-xdrfile-xtc" title="Permalink to this headline">¶</a></h1>
+<h1>5.21.1. Gromacs XTC trajectory I/O &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.xdrfile.XTC" title="MDAnalysis.coordinates.xdrfile.XTC"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.XTC</span></code></a><a class="headerlink" href="#gromacs-xtc-trajectory-i-o-mdanalysis-coordinates-xdrfile-xtc" title="Permalink to this headline">¶</a></h1>
 <p>Classes for reading and writing of <a class="reference external" href="http://www.gromacs.org/Documentation/File_Formats/.xtc_File">Gromacs XTC trajectories</a>
 together with supporting code.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">Users should access classes from <a class="reference internal" href="../XTC.html#module-MDAnalysis.coordinates.XTC" title="MDAnalysis.coordinates.XTC"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></tt></a>.</p>
+<p class="last">Users should access classes from <a class="reference internal" href="../XTC.html#module-MDAnalysis.coordinates.XTC" title="MDAnalysis.coordinates.XTC"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></code></a>.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.libxdrfile2</span></tt></a> for low-level
+<p class="last"><a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.libxdrfile2</span></code></a> for low-level
 bindings to the Gromacs trajectory file formats</p>
 </div>
 <div class="section" id="classes">
 <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.xdrfile.XTC.</tt><tt class="descname">Timestep</tt><big>(</big><em>n_atoms</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.xdrfile.XTC.</code><code class="descname">Timestep</code><span class="sig-paren">(</span><em>n_atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Timestep for a Gromacs trajectory.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Attributes status, lmbda, prec all stored in the <tt class="xref py py-attr docutils literal"><span class="pre">data</span></tt> dictionary
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Attributes status, lmbda, prec all stored in the <code class="xref py py-attr docutils literal"><span class="pre">data</span></code> dictionary
 Native frame number now stored as <cite>_frame</cite>, was <cite>step</cite></p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.copy">
-<tt class="descname">copy</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.copy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>.</p>
+<code class="descname">copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Make an independent (&#8220;deep&#8221;) copy of the whole <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.copy_slice">
-<tt class="descname">copy_slice</tt><big>(</big><em>sel</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
+<code class="descname">copy_slice</code><span class="sig-paren">(</span><em>sel</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/base.html#Timestep.copy_slice"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.copy_slice" title="Permalink to this definition">¶</a></dt>
 <dd><p>Make a new Timestep containing a subset of the original Timestep.</p>
-<p><tt class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></tt>
-<tt class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></tt></p>
+<p><code class="docutils literal"><span class="pre">ts.copy_slice(slice(start,</span> <span class="pre">stop,</span> <span class="pre">skip))</span></code>
+<code class="docutils literal"><span class="pre">ts.copy_slice([list</span> <span class="pre">of</span> <span class="pre">indices])</span></code></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A Timestep object of the same type containing all header
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A Timestep object of the same type containing all header
 information and all atom information relevant to the selection.</td>
 </tr>
 </tbody>
@@ -149,16 +150,18 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <p class="last">The selection must be a 0 based slice or array of the atom indices
 in this Timestep</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Reworked to follow new Timestep API.  Now will strictly only
 copy official attributes of the Timestep.</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.dimensions">
-<tt class="descname">dimensions</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>unitcell dimensions (A, B, C, alpha, beta, gamma)</p>
 <ul class="simple">
 <li>A, B, C are the lengths of the primitive cell vectors e1, e2, e3</li>
@@ -170,19 +173,20 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.dt" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dt</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.dt" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time difference in ps between timesteps</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">This defaults to 1.0 ps in the absence of time data</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.forces">
-<tt class="descname">forces</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.forces" title="Permalink to this definition">¶</a></dt>
+<code class="descname">forces</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.forces" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the forces of all atoms in this Timestep</p>
 <p>Setting this attribute will add forces to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -190,12 +194,12 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of force data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of force data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.NoDataError</span></tt></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.NoDataError</span></code></dt>
 <dd><p class="first last">When the Timestep does not contain force information</p>
 </dd>
 </dl>
@@ -203,67 +207,74 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
-<dl class="classmethod">
+<dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.from_coordinates">
-<em class="property">classmethod </em><tt class="descname">from_coordinates</tt><big>(</big><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
+<code class="descname">from_coordinates</code><span class="sig-paren">(</span><em>positions</em>, <em>velocities=None</em>, <em>forces=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_coordinates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.from_coordinates" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create an instance of this Timestep, from coordinate data</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
-<dl class="classmethod">
+<dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.from_timestep">
-<em class="property">classmethod </em><tt class="descname">from_timestep</tt><big>(</big><em>other</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">from_timestep</code><span class="sig-paren">(</span><em>other</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/base.html#Timestep.from_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.from_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a copy of another Timestep, in the format of this Timestep</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.has_forces">
-<tt class="descname">has_forces</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.has_forces" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_forces</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.has_forces" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has force data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.has_positions">
-<tt class="descname">has_positions</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.has_positions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_positions</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.has_positions" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has position data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.has_velocities">
-<tt class="descname">has_velocities</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.has_velocities" title="Permalink to this definition">¶</a></dt>
+<code class="descname">has_velocities</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.has_velocities" title="Permalink to this definition">¶</a></dt>
 <dd><p>A boolean of whether this Timestep has velocity data</p>
-<p>This can be changed to <tt class="docutils literal"><span class="pre">True</span></tt> or <tt class="docutils literal"><span class="pre">False</span></tt> to allocate space for
+<p>This can be changed to <code class="docutils literal"><span class="pre">True</span></code> or <code class="docutils literal"><span class="pre">False</span></code> to allocate space for
 or remove the data.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.n_atoms">
-<tt class="descname">n_atoms</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>A read only view of the number of atoms this Timestep has</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Changed to read only property</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.positions">
-<tt class="descname">positions</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.positions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">positions</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.positions" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the positions of all atoms in this Timestep</p>
 <p>Setting this attribute will add positions to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -271,12 +282,12 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of position data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of position data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><a class="reference internal" href="../../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></tt></a></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><a class="reference internal" href="../../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></code></a></dt>
 <dd><p class="first last">If the Timestep has no position data</p>
 </dd>
 </dl>
@@ -284,13 +295,14 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now can raise NoDataError when no position data present</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now can raise NoDataError when no position data present</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>The time in ps of this timestep</p>
 <p>This is calculated as:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">time</span>
@@ -300,19 +312,20 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <div class="highlight-python"><div class="highlight"><pre><span class="n">time</span> <span class="o">=</span> <span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s">&#39;time_offset&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span> <span class="o">*</span> <span class="n">ts</span><span class="o">.</span><span class="n">dt</span>
 </pre></div>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.triclinic_dimensions">
-<tt class="descname">triclinic_dimensions</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">triclinic_dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.triclinic_dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>The unitcell dimensions represented as triclinic vectors</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A (3, 3) numpy.ndarray of unit cell vectors</td>
 </tr>
 </tbody>
 </table>
@@ -332,17 +345,18 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <span class="go">        72.45159912,  71.56504822], dtype=float32)</span>
 </pre></div>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="../../lib/mdamath.html#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.mdamath.triclinic_vectors()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.velocities">
-<tt class="descname">velocities</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.velocities" title="Permalink to this definition">¶</a></dt>
+<code class="descname">velocities</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.velocities" title="Permalink to this definition">¶</a></dt>
 <dd><p>A record of the velocities of all atoms in this Timestep</p>
 <p>Setting this attribute will add velocities to the Timestep if they
 weren&#8217;t originally present.</p>
@@ -350,12 +364,12 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of velocity data for each
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A numpy.ndarray of shape (n_atoms, 3) of velocity data for each
 atom</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
-<dt><a class="reference internal" href="../../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></tt></a></dt>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><a class="reference internal" href="../../exceptions.html#MDAnalysis.exceptions.NoDataError" title="MDAnalysis.exceptions.NoDataError"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.exceptions.NoDataError</span></code></a></dt>
 <dd><p class="first last">When the Timestep does not contain velocity information</p>
 </dd>
 </dl>
@@ -363,13 +377,14 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.Timestep.volume">
-<tt class="descname">volume</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.volume" title="Permalink to this definition">¶</a></dt>
+<code class="descname">volume</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.volume" title="Permalink to this definition">¶</a></dt>
 <dd><p>volume of the unitcell</p>
 </dd></dl>
 
@@ -377,22 +392,23 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.xdrfile.XTC.</tt><tt class="descname">XTCReader</tt><big>(</big><em>filename</em>, <em>sub=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/XTC.html#XTCReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.xdrfile.XTC.</code><code class="descname">XTCReader</code><span class="sig-paren">(</span><em>filename</em>, <em>sub=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/XTC.html#XTCReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read <a class="reference external" href="http://www.gromacs.org">Gromacs</a> XTC trajectory.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Timestep attributes status and prec are now stored in the TS.data dictionary</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Timestep attributes status and prec are now stored in the TS.data dictionary</p>
+</div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">the name of the trr file.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>sub</em></dt>
 <dd><p class="first">an numpy integer array of what subset of trajectory atoms to load into
 the timestep. Intended to work similarly to the &#8216;sub&#8217; argument to <a class="reference external" href="http://www.gromacs.org">Gromacs</a>&#8216; trjconv.</p>
@@ -402,47 +418,50 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 equal to number of atoms in the Universe.</p>
 </dd>
 <dt><em>refresh_offsets</em></dt>
-<dd><p class="first last">if <tt class="docutils literal"><span class="pre">True</span></tt>, do not retrieve stored offsets, but instead generate
-new ones; if <tt class="docutils literal"><span class="pre">False</span></tt>, use retrieved offsets if available [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">if <code class="docutils literal"><span class="pre">True</span></code>, do not retrieve stored offsets, but instead generate
+new ones; if <code class="docutils literal"><span class="pre">False</span></code>, use retrieved offsets if available [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>refresh_offsets</em></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Renamed &#8220;delta&#8221; attribute to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>refresh_offsets</em></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Renamed &#8220;delta&#8221; attribute to &#8220;dt&#8221;
+Now passes weakref of self to ts (as &#8220;_reader&#8221;)</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.OtherWriter">
-<tt class="descname">OtherWriter</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">OtherWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.OtherWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a writer appropriate for <em>filename</em>.</p>
 <p>Sets the default keywords <em>start</em>, <em>step</em> and <em>dt</em> (if
-available). <em>n_atoms</em> is always set from <tt class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></tt>.</p>
-<div class="admonition-see-also admonition seealso">
+available). <em>n_atoms</em> is always set from <code class="xref py py-attr docutils literal"><span class="pre">Reader.n_atoms</span></code>.</p>
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></tt> and <tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></tt></p>
+<p class="last"><code class="xref py py-meth docutils literal"><span class="pre">Reader.Writer()</span></code> and <code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a Gromacs TrjWriter for <em>filename</em> with the same parameters as this trajectory.</p>
 <p>All values can be changed through keyword arguments.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">number of atoms</p>
 </dd>
@@ -456,132 +475,139 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">appropriate <tt class="xref py py-class docutils literal"><span class="pre">TrjWriter</span></tt></p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">appropriate <code class="xref py py-class docutils literal"><span class="pre">TrjWriter</span></code></p>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Changed &#8220;delta&#8221; keyword to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Changed &#8220;delta&#8221; keyword to &#8220;dt&#8221;</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close xdr trajectory file if it was open.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.dt" title="Permalink to this definition">¶</a></dt>
-<dd><p>Time step length in ps.</p>
-<p>The result is computed from the trajectory and cached. If for
-any reason the trajectory cannot be read then 0 is returned.</p>
+<code class="descname">dt</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.dt" title="Permalink to this definition">¶</a></dt>
+<dd><p>Time between two trajectory frames in picoseconds.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.frame">
-<tt class="descname">frame</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.frame" title="Permalink to this definition">¶</a></dt>
+<code class="descname">frame</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.frame" title="Permalink to this definition">¶</a></dt>
 <dd><p>Frame number of the current time step.</p>
-<p>This is a simple short cut to <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt>.</p>
+<p>This is a simple short cut to <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.load_offsets">
-<tt class="descname">load_offsets</tt><big>(</big><em>filename</em>, <em>check=False</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.load_offsets" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_offsets</code><span class="sig-paren">(</span><em>filename</em>, <em>check=False</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.load_offsets" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads current trajectory offsets from pickled <em>filename</em>.</p>
 <p>Checks if ctime and size of trajectory file matches that stored in
-pickled <em>filename</em>.  If either one does not match (and <em>check</em> == <tt class="docutils literal"><span class="pre">True</span></tt>)
+pickled <em>filename</em>.  If either one does not match (and <em>check</em> == <code class="docutils literal"><span class="pre">True</span></code>)
 then the offsets are not loaded.  This is intended to conservatively
 avoid loading out-of-date offsets.</p>
 <dl class="docutils">
@@ -600,22 +626,22 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
-<dd><p class="first last">filename of pickle file saved with <tt class="xref py py-meth docutils literal"><span class="pre">save_offsets()</span></tt> 
+<dd><p class="first last">filename of pickle file saved with <code class="xref py py-meth docutils literal"><span class="pre">save_offsets()</span></code> 
 with the frame offsets for the loaded trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>check</em></dt>
 <dd><p class="first last">if False, ignore ctime and size check of trajectory file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> if the file cannot be read (see <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">open()</span></tt></a>).</p>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> if the file cannot be read (see <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">open()</span></code></a>).</p>
 </td>
 </tr>
 </tbody>
@@ -624,7 +650,7 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.n_atoms">
-<tt class="descname">n_atoms</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>The number of publically available atoms that this reader will store in the timestep.</p>
 <p>If &#8216;sub&#8217; was not given in the ctor, then this value will just be the actual
 number of atoms in the underlying trajectory file. If however &#8216;sub&#8217; was given, then
@@ -634,7 +660,7 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.n_frames">
-<tt class="descname">n_frames</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.n_frames" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_frames</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.n_frames" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the number of frames from the trajectory.</p>
 <p>The result is cached. If for any reason the trajectory cannot
 be read then 0 is returned.</p>
@@ -642,29 +668,29 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 iterating through the whole trajectory. If the trajectory
 was previously loaded and saved offsets exist, then
 loading will be significantly faster.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-meth docutils literal"><span class="pre">TrjReader.load_offsets()</span></tt> and <tt class="xref py py-meth docutils literal"><span class="pre">TrjReader.save_offsets()</span></tt></p>
+<p class="last"><code class="xref py py-meth docutils literal"><span class="pre">TrjReader.load_offsets()</span></code> and <code class="xref py py-meth docutils literal"><span class="pre">TrjReader.save_offsets()</span></code></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.next">
-<tt class="descname">next</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.next" title="Permalink to this definition">¶</a></dt>
+<code class="descname">next</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.next" title="Permalink to this definition">¶</a></dt>
 <dd><p>Forward one step to next frame.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.open_trajectory">
-<tt class="descname">open_trajectory</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
+<code class="descname">open_trajectory</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
 <dd><p>Open xdr trajectory file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">pointer to XDRFILE (and sets self.xdrfile)</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">pointer to XDRFILE (and sets self.xdrfile)</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> with code EALREADY if file was already opened or
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> with code EALREADY if file was already opened or
 ENOENT if the file cannot be found</td>
 </tr>
 </tbody>
@@ -673,13 +699,13 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.rewind">
-<tt class="descname">rewind</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.rewind" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rewind</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.rewind" title="Permalink to this definition">¶</a></dt>
 <dd><p>Position at beginning of trajectory</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.save_offsets">
-<tt class="descname">save_offsets</tt><big>(</big><em>filename</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.save_offsets" title="Permalink to this definition">¶</a></dt>
+<code class="descname">save_offsets</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.save_offsets" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves current trajectory offsets into <em>filename</em>, as a pickled object.</p>
 <p>Along with the offsets themselves, the ctime and file size of the
 trajectory file are also saved.  These are used upon load as a check to
@@ -701,7 +727,7 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename in which to save the frame offsets</p>
 </dd>
@@ -714,15 +740,15 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.time">
-<tt class="descname">time</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.time" title="Permalink to this definition">¶</a></dt>
+<code class="descname">time</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.time" title="Permalink to this definition">¶</a></dt>
 <dd><p>Time of the current frame in MDAnalysis time units (typically ps).</p>
 <p>This is either read straight from the Timestep, or calculated as
-time = <tt class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></tt> * <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.dt" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep.dt"><tt class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></tt></a></p>
+time = <code class="xref py py-attr docutils literal"><span class="pre">Timestep.frame</span></code> * <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.dt" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep.dt"><code class="xref py py-attr docutils literal"><span class="pre">Timestep.dt</span></code></a></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCReader.totaltime">
-<tt class="descname">totaltime</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.totaltime" title="Permalink to this definition">¶</a></dt>
+<code class="descname">totaltime</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.totaltime" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total length of the trajectory n_frames * dt.</p>
 </dd></dl>
 
@@ -730,14 +756,14 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.xdrfile.XTC.</tt><tt class="descname">XTCWriter</tt><big>(</big><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=None</em>, <em>precision=1000.0</em>, <em>remarks=None</em>, <em>convert_units=None</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/XTC.html#XTCWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.xdrfile.XTC.</code><code class="descname">XTCWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=None</em>, <em>precision=1000.0</em>, <em>remarks=None</em>, <em>convert_units=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/XTC.html#XTCWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a <a class="reference external" href="http://www.gromacs.org">Gromacs</a> XTC trajectory.</p>
 <p>Create a new TrjWriter</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of output file</p>
 </dd>
@@ -747,7 +773,7 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>start</em></dt>
 <dd><p class="first last">starting timestep frame; only used when <em>dt</em> is set.</p>
 </dd>
@@ -756,9 +782,9 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 </dd>
 <dt><em>dt</em></dt>
 <dd><p class="first last">time between frames to use. If set will override any time information
-contained in the passed <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects, which will otherwise
+contained in the passed <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects, which will otherwise
 be used.
-The <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.time" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep.time"><tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt></a> attribute defaults to a timestep of
+The <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep.time" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep.time"><code class="xref py py-attr docutils literal"><span class="pre">time</span></code></a> attribute defaults to a timestep of
 to setting the trajectory time at 1 ps per step if there is no
 time information.</p>
 </dd>
@@ -767,121 +793,131 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 for TRR) [1000.0]</p>
 </dd>
 <dt><em>convert_units</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: units are converted to the MDAnalysis base format; <tt class="docutils literal"><span class="pre">None</span></tt> selects
-the value of <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> [&#8216;convert_lengths&#8217;].
-(see <a class="reference internal" href="../../core/init.html#flags-label"><em>Flags</em></a>)</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: units are converted to the MDAnalysis base format; <code class="docutils literal"><span class="pre">None</span></code> selects
+the value of <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> [&#8216;convert_lengths&#8217;].
+(see <a class="reference internal" href="../../core/init.html#flags-label"><span>Flags</span></a>)</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span>The TRR writer is now able to write TRRs without coordinates/velocities/forces,
-depending on the properties available in the <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects passed to
-<tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Keyword &#8220;delta&#8221; renamed to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span>The TRR writer is now able to write TRRs without coordinates/velocities/forces,
+depending on the properties available in the <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects passed to
+<code class="xref py py-meth docutils literal"><span class="pre">write()</span></code>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Keyword &#8220;delta&#8221; renamed to &#8220;dt&#8221;</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_dimensions_to_unitcell">
-<tt class="descname">convert_dimensions_to_unitcell</tt><big>(</big><em>ts</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_dimensions_to_unitcell</code><span class="sig-paren">(</span><em>ts</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read dimensions from timestep <em>ts</em> and return Gromacs box vectors</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.has_valid_coordinates">
-<tt class="descname">has_valid_coordinates</tt><big>(</big><em>criteria</em>, <em>x</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns <tt class="docutils literal"><span class="pre">True</span></tt> if all values are within limit values of their formats.</p>
+<code class="descname">has_valid_coordinates</code><span class="sig-paren">(</span><em>criteria</em>, <em>x</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.has_valid_coordinates" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns <code class="docutils literal"><span class="pre">True</span></code> if all values are within limit values of their formats.</p>
 <p>Due to rounding, the test is asymmetric (and <em>min</em> is supposed to be negative):</p>
 <blockquote>
 <div>min &lt; x &lt;= max</div></blockquote>
@@ -889,17 +925,17 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>criteria</em></dt>
 <dd><p class="first last">dictionary containing the <em>max</em> and <em>min</em> values in native units</p>
 </dd>
 <dt><em>x</em></dt>
-<dd><p class="first last"><tt class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></tt> of <tt class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></tt> coordinates of atoms selected to be written out.</p>
+<dd><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">np.ndarray</span></code> of <code class="docutils literal"><span class="pre">(x,</span> <span class="pre">y,</span> <span class="pre">z)</span></code> coordinates of atoms selected to be written out.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">boolean</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">boolean</p>
 </td>
 </tr>
 </tbody>
@@ -908,10 +944,10 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.write">
-<tt class="descname">write</tt><big>(</big><em>obj</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write current timestep, using the supplied <em>obj</em>.</p>
-<p>The argument should be a <a class="reference internal" href="../../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> or
-a <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> or a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance.</p>
+<p>The argument should be a <a class="reference internal" href="../../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> or
+a <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> or a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The size of the <em>obj</em> must be the same as the number of atom
@@ -921,9 +957,9 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.write_next_timestep">
-<tt class="descname">write_next_timestep</tt><big>(</big><em>ts=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_next_timestep</code><span class="sig-paren">(</span><em>ts=None</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>write a new timestep to the trj file</p>
-<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance containing coordinates to
+<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.XTC.Timestep" title="MDAnalysis.coordinates.xdrfile.XTC.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance containing coordinates to
 be written to trajectory file</p>
 </dd></dl>
 
@@ -938,7 +974,7 @@ <h2>5.21.1.1. Classes<a class="headerlink" href="#classes" title="Permalink to t
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -953,12 +989,12 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../xdrfile.html" title="5.21. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile"
              >previous</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
-          <li><a href="../xdrfile.html" >5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal docutils literal docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
+          <li class="nav-item nav-item-2"><a href="../xdrfile.html" >5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -968,7 +1004,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile/core.html b/package/doc/html/documentation_pages/coordinates/xdrfile/core.html
index f2efc100e82..6f7126850ce 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile/core.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile/core.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.21.3. Common high-level Gromacs XDR functionality — MDAnalysis.coordinates.xdrfile.core &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.21.3. Common high-level Gromacs XDR functionality — MDAnalysis.coordinates.xdrfile.core &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
     <link rel="up" title="5.21. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile" href="../xdrfile.html" />
     <link rel="next" title="5.21.4. The Gromacs XTC/TRR library libxdrfile2" href="libxdrfile2.html" />
     <link rel="prev" title="5.21.2. Gromacs TRR trajectory I/O — MDAnalysis.coordinates.xdrfile.TRR" href="TRR.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,19 +49,19 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="TRR.html" title="5.21.2. Gromacs TRR trajectory I/O — MDAnalysis.coordinates.xdrfile.TRR"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
-          <li><a href="../xdrfile.html" accesskey="U">5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
+          <li class="nav-item nav-item-2"><a href="../xdrfile.html" accesskey="U">5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.21.3. Common high-level Gromacs XDR functionality &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.core</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.21.3. Common high-level Gromacs XDR functionality &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.core</span></code></a><ul>
 <li><a class="reference internal" href="#generic-xdr-trj-classes">5.21.3.1. Generic xdr trj classes</a></li>
 </ul>
 </li>
@@ -71,16 +69,18 @@ <h3><a href="../../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="TRR.html"
-                        title="previous chapter">5.21.2. Gromacs TRR trajectory I/O &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.TRR</span></tt></a></p>
+                        title="previous chapter">5.21.2. Gromacs TRR trajectory I/O &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.TRR</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="libxdrfile2.html"
-                        title="next chapter">5.21.4. The Gromacs XTC/TRR library <tt class="docutils literal"><span class="pre">libxdrfile2</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../../_sources/documentation_pages/coordinates/xdrfile/core.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.21.4. The Gromacs XTC/TRR library <code class="docutils literal"><span class="pre">libxdrfile2</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../../_sources/documentation_pages/coordinates/xdrfile/core.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -99,34 +99,35 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.xdrfile.core"></span><div class="section" id="common-high-level-gromacs-xdr-functionality-mdanalysis-coordinates-xdrfile-core">
-<h1>5.21.3. Common high-level Gromacs XDR functionality &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.xdrfile.core" title="MDAnalysis.coordinates.xdrfile.core"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.core</span></tt></a><a class="headerlink" href="#common-high-level-gromacs-xdr-functionality-mdanalysis-coordinates-xdrfile-core" title="Permalink to this headline">¶</a></h1>
-<p>The <a class="reference internal" href="#module-MDAnalysis.coordinates.xdrfile.core" title="MDAnalysis.coordinates.xdrfile.core"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.core</span></tt></a> module contains generic
+<h1>5.21.3. Common high-level Gromacs XDR functionality &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.xdrfile.core" title="MDAnalysis.coordinates.xdrfile.core"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.core</span></code></a><a class="headerlink" href="#common-high-level-gromacs-xdr-functionality-mdanalysis-coordinates-xdrfile-core" title="Permalink to this headline">¶</a></h1>
+<p>The <a class="reference internal" href="#module-MDAnalysis.coordinates.xdrfile.core" title="MDAnalysis.coordinates.xdrfile.core"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.core</span></code></a> module contains generic
 classes to access <a class="reference external" href="http://www.gromacs.org">Gromacs</a> XDR-encoded trajectory formats such as TRR
 and XTC.</p>
 <p>A generic <a class="reference external" href="http://www.gromacs.org">Gromacs</a> trajectory is simply called &#8220;trj&#8221; within this
 module.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../base.html#module-MDAnalysis.coordinates.base" title="MDAnalysis.coordinates.base"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></tt></a> for the generic MDAnalysis base
-classes and <a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.libxdrfile2</span></tt></a> for
+<p class="last"><a class="reference internal" href="../base.html#module-MDAnalysis.coordinates.base" title="MDAnalysis.coordinates.base"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></code></a> for the generic MDAnalysis base
+classes and <a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.libxdrfile2</span></code></a> for
 the low-level bindings to the XDR trajectories.</p>
 </div>
 <div class="section" id="generic-xdr-trj-classes">
 <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-trj-classes" title="Permalink to this headline">¶</a></h2>
 <p>The generic classes are subclassed to generate the specific classes
 for the XTC and TRR format.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span>The XTC/TRR I/O interface now uses
-<a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt></a>, which has seeking and
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span>The XTC/TRR I/O interface now uses
+<a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code></a>, which has seeking and
 indexing capabilities. Note that unlike
-<tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></tt> before it,
-<a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt></a> is distributed under the
+<code class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></code> before it,
+<a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code></a> is distributed under the
 GNU GENERAL PUBLIC LICENSE, version 2 (or higher).</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>TrjReader now stores the offsets used for frame seeking automatically as a
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>TrjReader now stores the offsets used for frame seeking automatically as a
 hidden file in the same directory as the source trajectory. These offsets
 are automatically retrieved upon TrjReader instantiation, resulting in
 substantially quicker initialization times for long trajectories. The
@@ -134,18 +135,21 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 are checked against the trajectory on load to ensure the offsets aren&#8217;t
 stale. The offsets are automatically regenerated if they are stale or
 missing.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Frames now 0-based instead of 1-based</p>
+</div>
 <dl class="class">
 <dt id="MDAnalysis.coordinates.xdrfile.core.Timestep">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.xdrfile.core.</tt><tt class="descname">Timestep</tt><big>(</big><em>n_atoms</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.Timestep" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.xdrfile.core.</code><code class="descname">Timestep</code><span class="sig-paren">(</span><em>n_atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#Timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.Timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Timestep for a Gromacs trajectory.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Attributes status, lmbda, prec all stored in the <tt class="xref py py-attr docutils literal"><span class="pre">data</span></tt> dictionary
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Attributes status, lmbda, prec all stored in the <code class="xref py py-attr docutils literal"><span class="pre">data</span></code> dictionary
 Native frame number now stored as <cite>_frame</cite>, was <cite>step</cite></p>
+</div>
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.core.Timestep.dimensions">
-<tt class="descname">dimensions</tt><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#Timestep.dimensions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dimensions</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.Timestep.dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>unitcell dimensions (A, B, C, alpha, beta, gamma)</p>
 <ul class="simple">
 <li>A, B, C are the lengths of the primitive cell vectors e1, e2, e3</li>
@@ -159,9 +163,9 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.xdrfile.core.</tt><tt class="descname">TrjReader</tt><big>(</big><em>filename</em>, <em>sub=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.xdrfile.core.</code><code class="descname">TrjReader</code><span class="sig-paren">(</span><em>filename</em>, <em>sub=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Generic base class for reading Gromacs trajectories inside MDAnalysis.</p>
-<p>Derive classes and set <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.format" title="MDAnalysis.coordinates.xdrfile.core.TrjReader.format"><tt class="xref py py-attr docutils literal"><span class="pre">TrjReader.format</span></tt></a>, <tt class="xref py py-attr docutils literal"><span class="pre">TrjReader._read_trj</span></tt> and <tt class="xref py py-attr docutils literal"><span class="pre">TrjReader._read_trj_atoms</span></tt>.</p>
+<p>Derive classes and set <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.format" title="MDAnalysis.coordinates.xdrfile.core.TrjReader.format"><code class="xref py py-attr docutils literal"><span class="pre">TrjReader.format</span></code></a>, <code class="xref py py-attr docutils literal"><span class="pre">TrjReader._read_trj</span></code> and <code class="xref py py-attr docutils literal"><span class="pre">TrjReader._read_trj_atoms</span></code>.</p>
 <dl class="docutils">
 <dt>Example::</dt>
 <dd><p class="first">reader = TrjReader(&#8220;file.trj&#8221;)
@@ -174,14 +178,14 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">the name of the trr file.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>sub</em></dt>
 <dd><p class="first">an numpy integer array of what subset of trajectory atoms to load into
 the timestep. Intended to work similarly to the &#8216;sub&#8217; argument to <a class="reference external" href="http://www.gromacs.org">Gromacs</a>&#8216; trjconv.</p>
@@ -191,35 +195,38 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 equal to number of atoms in the Universe.</p>
 </dd>
 <dt><em>refresh_offsets</em></dt>
-<dd><p class="first last">if <tt class="docutils literal"><span class="pre">True</span></tt>, do not retrieve stored offsets, but instead generate
-new ones; if <tt class="docutils literal"><span class="pre">False</span></tt>, use retrieved offsets if available [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">if <code class="docutils literal"><span class="pre">True</span></code>, do not retrieve stored offsets, but instead generate
+new ones; if <code class="docutils literal"><span class="pre">False</span></code>, use retrieved offsets if available [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>refresh_offsets</em></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Renamed &#8220;delta&#8221; attribute to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>New keyword <em>refresh_offsets</em></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Renamed &#8220;delta&#8221; attribute to &#8220;dt&#8221;
+Now passes weakref of self to ts (as &#8220;_reader&#8221;)</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjReader.Writer">
-<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.Writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Writer</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.Writer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.Writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a Gromacs TrjWriter for <em>filename</em> with the same parameters as this trajectory.</p>
 <p>All values can be changed through keyword arguments.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename of the output trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>n_atoms</em></dt>
 <dd><p class="first last">number of atoms</p>
 </dd>
@@ -233,41 +240,34 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">appropriate <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter" title="MDAnalysis.coordinates.xdrfile.core.TrjWriter"><tt class="xref py py-class docutils literal"><span class="pre">TrjWriter</span></tt></a></p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">appropriate <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter" title="MDAnalysis.coordinates.xdrfile.core.TrjWriter"><code class="xref py py-class docutils literal"><span class="pre">TrjWriter</span></code></a></p>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Changed &#8220;delta&#8221; keyword to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Changed &#8220;delta&#8221; keyword to &#8220;dt&#8221;</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjReader.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close xdr trajectory file if it was open.</p>
 </dd></dl>
 
-<dl class="attribute">
-<dt id="MDAnalysis.coordinates.xdrfile.core.TrjReader.dt">
-<tt class="descname">dt</tt><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.dt"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.dt" title="Permalink to this definition">¶</a></dt>
-<dd><p>Time step length in ps.</p>
-<p>The result is computed from the trajectory and cached. If for
-any reason the trajectory cannot be read then 0 is returned.</p>
-</dd></dl>
-
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjReader.format">
-<tt class="descname">format</tt><em class="property"> = None</em><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.format" title="Permalink to this definition">¶</a></dt>
+<code class="descname">format</code><em class="property"> = None</em><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.format" title="Permalink to this definition">¶</a></dt>
 <dd><p>override to define trajectory format of the reader (XTC or TRR)</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjReader.load_offsets">
-<tt class="descname">load_offsets</tt><big>(</big><em>filename</em>, <em>check=False</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.load_offsets"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.load_offsets" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_offsets</code><span class="sig-paren">(</span><em>filename</em>, <em>check=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.load_offsets"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.load_offsets" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads current trajectory offsets from pickled <em>filename</em>.</p>
 <p>Checks if ctime and size of trajectory file matches that stored in
-pickled <em>filename</em>.  If either one does not match (and <em>check</em> == <tt class="docutils literal"><span class="pre">True</span></tt>)
+pickled <em>filename</em>.  If either one does not match (and <em>check</em> == <code class="docutils literal"><span class="pre">True</span></code>)
 then the offsets are not loaded.  This is intended to conservatively
 avoid loading out-of-date offsets.</p>
 <dl class="docutils">
@@ -286,22 +286,22 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
-<dd><p class="first last">filename of pickle file saved with <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets" title="MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets"><tt class="xref py py-meth docutils literal"><span class="pre">save_offsets()</span></tt></a> 
+<dd><p class="first last">filename of pickle file saved with <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets" title="MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets"><code class="xref py py-meth docutils literal"><span class="pre">save_offsets()</span></code></a> 
 with the frame offsets for the loaded trajectory</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>check</em></dt>
 <dd><p class="first last">if False, ignore ctime and size check of trajectory file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> if the file cannot be read (see <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">open()</span></tt></a>).</p>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> if the file cannot be read (see <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">open()</span></code></a>).</p>
 </td>
 </tr>
 </tbody>
@@ -310,7 +310,7 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjReader.n_atoms">
-<tt class="descname">n_atoms</tt><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.n_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>The number of publically available atoms that this reader will store in the timestep.</p>
 <p>If &#8216;sub&#8217; was not given in the ctor, then this value will just be the actual
 number of atoms in the underlying trajectory file. If however &#8216;sub&#8217; was given, then
@@ -320,7 +320,7 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjReader.n_frames">
-<tt class="descname">n_frames</tt><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.n_frames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.n_frames" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_frames</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.n_frames" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the number of frames from the trajectory.</p>
 <p>The result is cached. If for any reason the trajectory cannot
 be read then 0 is returned.</p>
@@ -328,23 +328,23 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 iterating through the whole trajectory. If the trajectory
 was previously loaded and saved offsets exist, then
 loading will be significantly faster.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.load_offsets" title="MDAnalysis.coordinates.xdrfile.core.TrjReader.load_offsets"><tt class="xref py py-meth docutils literal"><span class="pre">TrjReader.load_offsets()</span></tt></a> and <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets" title="MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets"><tt class="xref py py-meth docutils literal"><span class="pre">TrjReader.save_offsets()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.load_offsets" title="MDAnalysis.coordinates.xdrfile.core.TrjReader.load_offsets"><code class="xref py py-meth docutils literal"><span class="pre">TrjReader.load_offsets()</span></code></a> and <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets" title="MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets"><code class="xref py py-meth docutils literal"><span class="pre">TrjReader.save_offsets()</span></code></a></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjReader.open_trajectory">
-<tt class="descname">open_trajectory</tt><big>(</big><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.open_trajectory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
+<code class="descname">open_trajectory</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.open_trajectory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.open_trajectory" title="Permalink to this definition">¶</a></dt>
 <dd><p>Open xdr trajectory file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">pointer to XDRFILE (and sets self.xdrfile)</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">pointer to XDRFILE (and sets self.xdrfile)</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> with code EALREADY if file was already opened or
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> with code EALREADY if file was already opened or
 ENOENT if the file cannot be found</td>
 </tr>
 </tbody>
@@ -353,7 +353,7 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets">
-<tt class="descname">save_offsets</tt><big>(</big><em>filename</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.save_offsets"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets" title="Permalink to this definition">¶</a></dt>
+<code class="descname">save_offsets</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjReader.save_offsets"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.save_offsets" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves current trajectory offsets into <em>filename</em>, as a pickled object.</p>
 <p>Along with the offsets themselves, the ctime and file size of the
 trajectory file are also saved.  These are used upon load as a check to
@@ -375,7 +375,7 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">filename in which to save the frame offsets</p>
 </dd>
@@ -388,7 +388,7 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjReader.units">
-<tt class="descname">units</tt><em class="property"> = {'length': 'nm', 'time': 'ps'}</em><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.units" title="Permalink to this definition">¶</a></dt>
+<code class="descname">units</code><em class="property"> = {'length': 'nm', 'time': 'ps'}</em><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjReader.units" title="Permalink to this definition">¶</a></dt>
 <dd><p>units of time (ps) and length (nm) in Gromacs</p>
 </dd></dl>
 
@@ -396,7 +396,7 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 
 <dl class="class">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.xdrfile.core.</tt><tt class="descname">TrjWriter</tt><big>(</big><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=None</em>, <em>precision=1000.0</em>, <em>remarks=None</em>, <em>convert_units=None</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.coordinates.xdrfile.core.</code><code class="descname">TrjWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>n_atoms</em>, <em>start=0</em>, <em>step=1</em>, <em>dt=None</em>, <em>precision=1000.0</em>, <em>remarks=None</em>, <em>convert_units=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Writes to a Gromacs trajectory file</p>
 <p>(Base class)</p>
 <p>Create a new TrjWriter</p>
@@ -404,7 +404,7 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of output file</p>
 </dd>
@@ -414,7 +414,7 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>start</em></dt>
 <dd><p class="first last">starting timestep frame; only used when <em>dt</em> is set.</p>
 </dd>
@@ -423,9 +423,9 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 </dd>
 <dt><em>dt</em></dt>
 <dd><p class="first last">time between frames to use. If set will override any time information
-contained in the passed <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.Timestep" title="MDAnalysis.coordinates.xdrfile.core.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects, which will otherwise
+contained in the passed <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.Timestep" title="MDAnalysis.coordinates.xdrfile.core.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects, which will otherwise
 be used.
-The <tt class="xref py py-attr docutils literal"><span class="pre">time</span></tt> attribute defaults to a timestep of
+The <code class="xref py py-attr docutils literal"><span class="pre">time</span></code> attribute defaults to a timestep of
 to setting the trajectory time at 1 ps per step if there is no
 time information.</p>
 </dd>
@@ -434,44 +434,46 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
 for TRR) [1000.0]</p>
 </dd>
 <dt><em>convert_units</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: units are converted to the MDAnalysis base format; <tt class="docutils literal"><span class="pre">None</span></tt> selects
-the value of <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> [&#8216;convert_lengths&#8217;].
-(see <a class="reference internal" href="../../core/init.html#flags-label"><em>Flags</em></a>)</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: units are converted to the MDAnalysis base format; <code class="docutils literal"><span class="pre">None</span></code> selects
+the value of <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> [&#8216;convert_lengths&#8217;].
+(see <a class="reference internal" href="../../core/init.html#flags-label"><span>Flags</span></a>)</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span>The TRR writer is now able to write TRRs without coordinates/velocities/forces,
-depending on the properties available in the <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.Timestep" title="MDAnalysis.coordinates.xdrfile.core.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> objects passed to
-<tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Keyword &#8220;delta&#8221; renamed to &#8220;dt&#8221;</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span>The TRR writer is now able to write TRRs without coordinates/velocities/forces,
+depending on the properties available in the <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.Timestep" title="MDAnalysis.coordinates.xdrfile.core.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> objects passed to
+<code class="xref py py-meth docutils literal"><span class="pre">write()</span></code>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Keyword &#8220;delta&#8221; renamed to &#8220;dt&#8221;</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjWriter.convert_dimensions_to_unitcell">
-<tt class="descname">convert_dimensions_to_unitcell</tt><big>(</big><em>ts</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjWriter.convert_dimensions_to_unitcell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_dimensions_to_unitcell</code><span class="sig-paren">(</span><em>ts</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjWriter.convert_dimensions_to_unitcell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter.convert_dimensions_to_unitcell" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read dimensions from timestep <em>ts</em> and return Gromacs box vectors</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjWriter.format">
-<tt class="descname">format</tt><em class="property"> = None</em><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter.format" title="Permalink to this definition">¶</a></dt>
+<code class="descname">format</code><em class="property"> = None</em><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter.format" title="Permalink to this definition">¶</a></dt>
 <dd><p>override to define trajectory format of the reader (XTC or TRR)</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjWriter.units">
-<tt class="descname">units</tt><em class="property"> = {'length': 'nm', 'time': 'ps'}</em><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter.units" title="Permalink to this definition">¶</a></dt>
+<code class="descname">units</code><em class="property"> = {'length': 'nm', 'time': 'ps'}</em><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter.units" title="Permalink to this definition">¶</a></dt>
 <dd><p>units of time (ps) and length (nm) in Gromacs</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.coordinates.xdrfile.core.TrjWriter.write_next_timestep">
-<tt class="descname">write_next_timestep</tt><big>(</big><em>ts=None</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjWriter.write_next_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_next_timestep</code><span class="sig-paren">(</span><em>ts=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/core.html#TrjWriter.write_next_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.core.TrjWriter.write_next_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>write a new timestep to the trj file</p>
-<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.Timestep" title="MDAnalysis.coordinates.xdrfile.core.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance containing coordinates to
+<p><em>ts</em> is a <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.core.Timestep" title="MDAnalysis.coordinates.xdrfile.core.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance containing coordinates to
 be written to trajectory file</p>
 </dd></dl>
 
@@ -486,7 +488,7 @@ <h2>5.21.3.1. Generic xdr trj classes<a class="headerlink" href="#generic-xdr-tr
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -501,12 +503,12 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="TRR.html" title="5.21.2. Gromacs TRR trajectory I/O — MDAnalysis.coordinates.xdrfile.TRR"
              >previous</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
-          <li><a href="../xdrfile.html" >5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
+          <li class="nav-item nav-item-2"><a href="../xdrfile.html" >5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -516,7 +518,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile/libxdrfile2.html b/package/doc/html/documentation_pages/coordinates/xdrfile/libxdrfile2.html
index d5f9020f7d0..bb37c7954ac 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile/libxdrfile2.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile/libxdrfile2.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.21.4. The Gromacs XTC/TRR library libxdrfile2 &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.21.4. The Gromacs XTC/TRR library libxdrfile2 &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
     <link rel="up" title="5.21. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile" href="../xdrfile.html" />
     <link rel="next" title="5.21.5. Status codes and symbols — statno" href="statno.html" />
     <link rel="prev" title="5.21.3. Common high-level Gromacs XDR functionality — MDAnalysis.coordinates.xdrfile.core" href="core.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
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-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
-          <li><a href="../xdrfile.html" accesskey="U">5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
+          <li class="nav-item nav-item-2"><a href="../xdrfile.html" accesskey="U">5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a> &raquo;</li> 
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
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   <h3><a href="../../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">5.21.4. The Gromacs XTC/TRR library <tt class="docutils literal"><span class="pre">libxdrfile2</span></tt></a><ul>
+<li><a class="reference internal" href="#">5.21.4. The Gromacs XTC/TRR library <code class="docutils literal"><span class="pre">libxdrfile2</span></code></a><ul>
 <li><a class="reference internal" href="#example-reading-from-a-xtc">5.21.4.1. Example: Reading from a XTC</a></li>
 <li><a class="reference internal" href="#functions-and-constants">5.21.4.2. Functions and constants</a><ul>
 <li><a class="reference internal" href="#status-symbols">5.21.4.2.1. Status symbols</a></li>
@@ -78,16 +76,18 @@ <h3><a href="../../../index.html">Table Of Contents</a></h3>
 
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+                        title="previous chapter">5.21.3. Common high-level Gromacs XDR functionality &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile.core</span></code></a></p>
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+                        title="next chapter">5.21.5. Status codes and symbols &#8212; <code class="docutils literal"><span class="pre">statno</span></code></a></p>
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+    <h3>This Page</h3>
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   <span class="target" id="module-MDAnalysis.coordinates.xdrfile.libxdrfile2"></span><div class="section" id="the-gromacs-xtc-trr-library-libxdrfile2">
-<h1>5.21.4. The Gromacs XTC/TRR library <tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt><a class="headerlink" href="#the-gromacs-xtc-trr-library-libxdrfile2" title="Permalink to this headline">¶</a></h1>
-<p><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt>, a derivative of the <a class="reference external" href="http://www.gromacs.org">Gromacs</a> <a class="reference external" href="http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library">libxdrfile library</a>, provides an
+<h1>5.21.4. The Gromacs XTC/TRR library <code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code><a class="headerlink" href="#the-gromacs-xtc-trr-library-libxdrfile2" title="Permalink to this headline">¶</a></h1>
+<p><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code>, a derivative of the <a class="reference external" href="http://www.gromacs.org">Gromacs</a> <a class="reference external" href="http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library">libxdrfile library</a>, provides an
 interface to some high-level functions for XTC/TRR trajectory handling.
 Only functions required for reading and processing whole trajectories are exposed at
 the moment; low-level routines to read individual numbers are not provided. In
-addition, <tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt> exposes functions to allow fast frame indexing and XDR
+addition, <code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code> exposes functions to allow fast frame indexing and XDR
 file seeking.</p>
 <p>The functions querying the numbers of atoms in a trajectory frame
-(<a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_natoms" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_natoms"><tt class="xref py py-func docutils literal"><span class="pre">read_xtc_natoms()</span></tt></a> and <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_natoms" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_natoms"><tt class="xref py py-func docutils literal"><span class="pre">read_trr_natoms()</span></tt></a>) open a file themselves and
+(<a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_natoms" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_natoms"><code class="xref py py-func docutils literal"><span class="pre">read_xtc_natoms()</span></code></a> and <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_natoms" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_natoms"><code class="xref py py-func docutils literal"><span class="pre">read_trr_natoms()</span></code></a>) open a file themselves and
 only require the file name.</p>
 <p>All other functions operate on a <em>XDRFILE</em> object, which is a special file
 handle for xdr files.  Any xdr-based trajectory file (XTC or TRR format) always
-has to be opened with <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_open" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_open"><tt class="xref py py-func docutils literal"><span class="pre">xdrfile_open()</span></tt></a>. When done, close the trajectory
-with <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_close" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_close"><tt class="xref py py-func docutils literal"><span class="pre">xdrfile_close()</span></tt></a>.</p>
+has to be opened with <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_open" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_open"><code class="xref py py-func docutils literal"><span class="pre">xdrfile_open()</span></code></a>. When done, close the trajectory
+with <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_close" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_close"><code class="xref py py-func docutils literal"><span class="pre">xdrfile_close()</span></code></a>.</p>
 <p>The functions fill or read existing arrays of coordinates; they never allocate
 these arrays themselves. Hence they need to be setup outside libxdrfile2 as
 numpy arrays. The exception to these are the indexing ones functions that take
 care of array allocation and transference to a garbage-collectable memory object.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt> is now used instead of <tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></tt>. <tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt> is
-based on <tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></tt> but has xdr seeking and indexing capabilities.
-Unlike <tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></tt> before it, <tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt> is distributed under the GNU
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code> is now used instead of <code class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></code>. <code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code> is
+based on <code class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></code> but has xdr seeking and indexing capabilities.
+Unlike <code class="xref py py-mod docutils literal"><span class="pre">libxdrfile</span></code> before it, <code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code> is distributed under the GNU
 GENERAL PUBLIC LICENSE, version 2 (or higher).</p>
+</div>
 <div class="section" id="example-reading-from-a-xtc">
 <h2>5.21.4.1. Example: Reading from a XTC<a class="headerlink" href="#example-reading-from-a-xtc" title="Permalink to this headline">¶</a></h2>
 <p>In the example we read coordinate frames from an existing XTC trajectory:</p>
@@ -169,11 +170,11 @@ <h2>5.21.4.1. Example: Reading from a XTC<a class="headerlink" href="#example-re
 </div>
 <div class="section" id="functions-and-constants">
 <h2>5.21.4.2. Functions and constants<a class="headerlink" href="#functions-and-constants" title="Permalink to this headline">¶</a></h2>
-<p>The module defines a number of constants such as <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.DIM" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.DIM"><tt class="xref py py-data docutils literal"><span class="pre">DIM</span></tt></a> or the
+<p>The module defines a number of constants such as <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.DIM" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.DIM"><code class="xref py py-data docutils literal"><span class="pre">DIM</span></code></a> or the
 <a class="reference internal" href="#status-symbols">Status symbols</a>.</p>
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.DIM">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">DIM</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.DIM" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">DIM</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.DIM" title="Permalink to this definition">¶</a></dt>
 <dd><p>The number of cartesian dimensions for which the underlying C-code
 was compiled; this is most certainly 3.</p>
 </dd></dl>
@@ -181,84 +182,84 @@ <h2>5.21.4.2. Functions and constants<a class="headerlink" href="#functions-and-
 <div class="section" id="status-symbols">
 <h3>5.21.4.2.1. Status symbols<a class="headerlink" href="#status-symbols" title="Permalink to this headline">¶</a></h3>
 <p>A number of symbols are exported; they all start with the letters
-<tt class="docutils literal"><span class="pre">exdr</span></tt>. Important ones are:</p>
+<code class="docutils literal"><span class="pre">exdr</span></code>. Important ones are:</p>
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrOK">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrOK</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrOK" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrOK</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrOK" title="Permalink to this definition">¶</a></dt>
 <dd><p>Success of xdr file read/write operation.</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrCLOSE">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrCLOSE</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrCLOSE" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrCLOSE</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrCLOSE" title="Permalink to this definition">¶</a></dt>
 <dd><p>xdr file is closed</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrENDOFFILE">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrENDOFFILE</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrENDOFFILE" title="Permalink to this definition">¶</a></dt>
-<dd><p>end of file was reached (response of <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc"><tt class="xref py py-func docutils literal"><span class="pre">read_xtc()</span></tt></a> and
-<a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr"><tt class="xref py py-func docutils literal"><span class="pre">read_trr()</span></tt></a> after the last read frame)</p>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrENDOFFILE</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrENDOFFILE" title="Permalink to this definition">¶</a></dt>
+<dd><p>end of file was reached (response of <a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc"><code class="xref py py-func docutils literal"><span class="pre">read_xtc()</span></code></a> and
+<a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr"><code class="xref py py-func docutils literal"><span class="pre">read_trr()</span></code></a> after the last read frame)</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrFILENOTFOUND">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrFILENOTFOUND</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrFILENOTFOUND" title="Permalink to this definition">¶</a></dt>
-<dd><p><a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_open" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_open"><tt class="xref py py-func docutils literal"><span class="pre">xdrfile_open()</span></tt></a> cannot find the requested file</p>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrFILENOTFOUND</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrFILENOTFOUND" title="Permalink to this definition">¶</a></dt>
+<dd><p><a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_open" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_open"><code class="xref py py-func docutils literal"><span class="pre">xdrfile_open()</span></code></a> cannot find the requested file</p>
 </dd></dl>
 
 <p>Other symbols that are used internally are:</p>
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrHEADER">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrHEADER</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrHEADER" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrHEADER</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrHEADER" title="Permalink to this definition">¶</a></dt>
 <dd><p>header</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrSTRING">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrSTRING</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrSTRING" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrSTRING</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrSTRING" title="Permalink to this definition">¶</a></dt>
 <dd><p>string</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrDOUBLE">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrDOUBLE</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrDOUBLE" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrDOUBLE</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrDOUBLE" title="Permalink to this definition">¶</a></dt>
 <dd><p>double precision floating point number</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrINT">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrINT</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrINT" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrINT</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrINT" title="Permalink to this definition">¶</a></dt>
 <dd><p>integer</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrFLOAT">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrFLOAT</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrFLOAT" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrFLOAT</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrFLOAT" title="Permalink to this definition">¶</a></dt>
 <dd><p>floating point number</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrUINT">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrUINT</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrUINT" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrUINT</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrUINT" title="Permalink to this definition">¶</a></dt>
 <dd><p>unsigned integer</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdr3DX">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdr3DX</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdr3DX" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdr3DX</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdr3DX" title="Permalink to this definition">¶</a></dt>
 <dd><p>compressed 3D coordinates</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrMAGIC">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrMAGIC</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrMAGIC" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrMAGIC</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrMAGIC" title="Permalink to this definition">¶</a></dt>
 <dd><p>magic number</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrNOMEM">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">exdrNOMEM</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrNOMEM" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">exdrNOMEM</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.exdrNOMEM" title="Permalink to this definition">¶</a></dt>
 <dd><p>not enough memory to allocate space for a XDR data structure.</p>
 </dd></dl>
 
@@ -269,7 +270,7 @@ <h3>5.21.4.2.2. Opening and closing of XDR files<a class="headerlink" href="#ope
 to access xdr files such as XTC or TRR trajectories.</p>
 <dl class="function">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_open">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">xdrfile_open</tt><big>(</big><em>path</em>, <em>mode</em><big>)</big> &rarr; XDRFILE<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#xdrfile_open"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_open" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">xdrfile_open</code><span class="sig-paren">(</span><em>path</em>, <em>mode</em><span class="sig-paren">)</span> &rarr; XDRFILE<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#xdrfile_open"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_open" title="Permalink to this definition">¶</a></dt>
 <dd><blockquote>
 <div><p>Open <em>path</em> and returns a <em>XDRFILE</em> handle that is required by other
 functions.</p>
@@ -292,7 +293,7 @@ <h3>5.21.4.2.2. Opening and closing of XDR files<a class="headerlink" href="#ope
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><em>XDRFILE</em> handle</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><em>XDRFILE</em> handle</td>
 </tr>
 </tbody>
 </table>
@@ -300,7 +301,7 @@ <h3>5.21.4.2.2. Opening and closing of XDR files<a class="headerlink" href="#ope
 
 <dl class="function">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_close">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">xdrfile_close</tt><big>(</big><em>XDRFILE</em><big>)</big> &rarr; status<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#xdrfile_close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_close" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">xdrfile_close</code><span class="sig-paren">(</span><em>XDRFILE</em><span class="sig-paren">)</span> &rarr; status<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#xdrfile_close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.xdrfile_close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the xdrfile pointed to by <em>XDRFILE</em>.</p>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
@@ -314,26 +315,26 @@ <h3>5.21.4.2.2. Opening and closing of XDR files<a class="headerlink" href="#ope
 <h3>5.21.4.2.3. XTC functions<a class="headerlink" href="#xtc-functions" title="Permalink to this headline">¶</a></h3>
 <p>The XTC trajectory format is a lossy compression format that only stores
 coordinates. Compression level is determined by the <em>precision</em> argument to the
-<a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.write_xtc" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.write_xtc"><tt class="xref py py-func docutils literal"><span class="pre">write_xtc()</span></tt></a> function. Coordinates (<a class="reference external" href="http://www.gromacs.org">Gromacs</a> uses nm natively) are
+<a class="reference internal" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.write_xtc" title="MDAnalysis.coordinates.xdrfile.libxdrfile2.write_xtc"><code class="xref py py-func docutils literal"><span class="pre">write_xtc()</span></code></a> function. Coordinates (<a class="reference external" href="http://www.gromacs.org">Gromacs</a> uses nm natively) are
 multiplied by <em>precision</em> and truncated to the integer part. A typical value is
 1000.0, which gives an accuracy of 1/100 of an Angstroem.</p>
 <p>The advantage of XTC over TRR is its significantly reduced size.</p>
 <dl class="function">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_natoms">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">read_xtc_natoms</tt><big>(</big><em>fn</em><big>)</big> &rarr; natoms<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_xtc_natoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_natoms" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">read_xtc_natoms</code><span class="sig-paren">(</span><em>fn</em><span class="sig-paren">)</span> &rarr; natoms<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_xtc_natoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_natoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the number of atoms <em>natoms</em> from a xtc file <em>fn</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>fn</em></dt>
 <dd><p class="first last">file name of an xtc file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> if the supplied filed is not a XTC 
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> if the supplied filed is not a XTC 
 or if it is not readable.</p>
 </td>
 </tr>
@@ -343,7 +344,7 @@ <h3>5.21.4.2.3. XTC functions<a class="headerlink" href="#xtc-functions" title="
 
 <dl class="function">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_n_frames">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">read_xtc_n_frames</tt><big>(</big><em>fn) -&gt; (n_frames</em>, <em>offsets</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_xtc_n_frames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_n_frames" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">read_xtc_n_frames</code><span class="sig-paren">(</span><em>fn) -&gt; (n_frames</em>, <em>offsets</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_xtc_n_frames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_n_frames" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read through the whole trajectory headers to obtain the total number of frames. 
 The process is speeded up by reading frame headers for the amount of data in the frame,
 and then skipping directly to the next header. An array of frame offsets is also
@@ -352,14 +353,14 @@ <h3>5.21.4.2.3. XTC functions<a class="headerlink" href="#xtc-functions" title="
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>fn</em></dt>
 <dd><p class="first last">file name of an xtc file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first docutils">
 <dt>a tuple containing:</dt>
 <dd><dl class="first last docutils">
 <dt><em>n_frames</em></dt>
@@ -373,7 +374,7 @@ <h3>5.21.4.2.3. XTC functions<a class="headerlink" href="#xtc-functions" title="
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> if the supplied filed is not a XTC 
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> if the supplied filed is not a XTC 
 or if it is not readable.</p>
 </td>
 </tr>
@@ -383,28 +384,28 @@ <h3>5.21.4.2.3. XTC functions<a class="headerlink" href="#xtc-functions" title="
 
 <dl class="function">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">read_xtc</tt><big>(</big><em>XDRFILE</em>, <em>box</em>, <em>x) -&gt; (status</em>, <em>step</em>, <em>time</em>, <em>precision</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_xtc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">read_xtc</code><span class="sig-paren">(</span><em>XDRFILE</em>, <em>box</em>, <em>x) -&gt; (status</em>, <em>step</em>, <em>time</em>, <em>precision</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_xtc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the next frame from the opened xtc trajectory into <em>x</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>XDRFILE</em></dt>
 <dd><p class="first last">open <em>XDRFILE</em> object</p>
 </dd>
 <dt><em>box</em></dt>
-<dd><p class="first last">pre-allocated numpy <tt class="docutils literal"><span class="pre">array((DIM,DIM),dtype=numpy.float32)</span></tt> which
+<dd><p class="first last">pre-allocated numpy <code class="docutils literal"><span class="pre">array((DIM,DIM),dtype=numpy.float32)</span></code> which
 is filled with the unit cell box vectors</p>
 </dd>
 <dt><em>x</em></dt>
-<dd><p class="first last">pre-allocated numpy <tt class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=numpy.float32)</span></tt>
+<dd><p class="first last">pre-allocated numpy <code class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=numpy.float32)</span></code>
 which is updated with the coordinates from the frame</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt>a tuple containing:</dt>
 <dd><dl class="first last docutils">
 <dt><em>status</em></dt>
@@ -431,13 +432,13 @@ <h3>5.21.4.2.3. XTC functions<a class="headerlink" href="#xtc-functions" title="
 
 <dl class="function">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.write_xtc">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">write_xtc</tt><big>(</big><em>XDRFILE</em>, <em>step</em>, <em>time</em>, <em>box</em>, <em>x</em>, <em>prec</em><big>)</big> &rarr; status<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#write_xtc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.write_xtc" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">write_xtc</code><span class="sig-paren">(</span><em>XDRFILE</em>, <em>step</em>, <em>time</em>, <em>box</em>, <em>x</em>, <em>prec</em><span class="sig-paren">)</span> &rarr; status<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#write_xtc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.write_xtc" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write the next frame <em>x</em> to the opened xtc trajectory.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>XDRFILE</em></dt>
 <dd><p class="first last">open <em>XDRFILE</em> object (writable)</p>
 </dd>
@@ -448,11 +449,11 @@ <h3>5.21.4.2.3. XTC functions<a class="headerlink" href="#xtc-functions" title="
 <dd><p class="first last">time step in ps</p>
 </dd>
 <dt><em>box</em></dt>
-<dd><p class="first last">numpy <tt class="docutils literal"><span class="pre">array((DIM,DIM),dtype=numpy.float32)</span></tt> which contains 
+<dd><p class="first last">numpy <code class="docutils literal"><span class="pre">array((DIM,DIM),dtype=numpy.float32)</span></code> which contains 
 the unit cell box vectors</p>
 </dd>
 <dt><em>x</em></dt>
-<dd><p class="first last">numpy <tt class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></tt>
+<dd><p class="first last">numpy <code class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></code>
 which contains the coordinates from the frame</p>
 </dd>
 <dt><em>precision</em></dt>
@@ -461,7 +462,7 @@ <h3>5.21.4.2.3. XTC functions<a class="headerlink" href="#xtc-functions" title="
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><em>status</em>, integer status (0 = OK), see the <tt class="docutils literal"><span class="pre">libxdrfile2.exdr*</span></tt> 
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><em>status</em>, integer status (0 = OK), see the <code class="docutils literal"><span class="pre">libxdrfile2.exdr*</span></code> 
 constants under <a class="reference internal" href="#status-symbols">Status symbols</a> for other values)</p>
 </td>
 </tr>
@@ -477,20 +478,20 @@ <h3>5.21.4.2.4. TRR functions<a class="headerlink" href="#trr-functions" title="
 calculations. Velocities and forces are optional in the sense that they can be all zero.</p>
 <dl class="function">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_natoms">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">read_trr_natoms</tt><big>(</big><em>fn</em><big>)</big> &rarr; natoms<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_trr_natoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_natoms" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">read_trr_natoms</code><span class="sig-paren">(</span><em>fn</em><span class="sig-paren">)</span> &rarr; natoms<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_trr_natoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_natoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the number of atoms <em>natoms</em> from a trr file <em>fn</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>fn</em></dt>
 <dd><p class="first last">file name of a trr file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> if the supplied filed is not a TRR
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> if the supplied filed is not a TRR
 or if it is not readable.</p>
 </td>
 </tr>
@@ -500,7 +501,7 @@ <h3>5.21.4.2.4. TRR functions<a class="headerlink" href="#trr-functions" title="
 
 <dl class="function">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_n_frames">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">read_trr_n_frames</tt><big>(</big><em>fn) -&gt; (n_frames</em>, <em>offsets</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_trr_n_frames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_n_frames" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">read_trr_n_frames</code><span class="sig-paren">(</span><em>fn) -&gt; (n_frames</em>, <em>offsets</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_trr_n_frames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr_n_frames" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read through the whole trajectory headers to obtain the total number of frames. 
 The process is speeded up by reading frame headers for the amount of data in the frame,
 and then skipping directly to the next header. An array of frame offsets is also
@@ -509,14 +510,14 @@ <h3>5.21.4.2.4. TRR functions<a class="headerlink" href="#trr-functions" title="
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>fn</em></dt>
 <dd><p class="first last">file name of an xtc file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first docutils">
 <dt>a tuple containing:</dt>
 <dd><dl class="first last docutils">
 <dt><em>n_frames</em></dt>
@@ -530,7 +531,7 @@ <h3>5.21.4.2.4. TRR functions<a class="headerlink" href="#trr-functions" title="
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> if the supplied filed is not a TRR or if it is not readable.</p>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> if the supplied filed is not a TRR or if it is not readable.</p>
 </td>
 </tr>
 </tbody>
@@ -539,40 +540,40 @@ <h3>5.21.4.2.4. TRR functions<a class="headerlink" href="#trr-functions" title="
 
 <dl class="function">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">read_trr</tt><big>(</big><em>XDRFILE</em>, <em>box</em>, <em>x</em>, <em>v</em>, <em>f) -&gt; (status</em>, <em>step</em>, <em>time</em>, <em>lambda</em><big>)</big><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_trr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">read_trr</code><span class="sig-paren">(</span><em>XDRFILE</em>, <em>box</em>, <em>x</em>, <em>v</em>, <em>f) -&gt; (status</em>, <em>step</em>, <em>time</em>, <em>lambda</em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#read_trr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.read_trr" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the next frame from the opened trr trajectory into <em>x</em>, <em>v</em>, and <em>f</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>XDRFILE</em></dt>
 <dd><p class="first last">open <em>XDRFILE</em> object</p>
 </dd>
 <dt><em>box</em></dt>
-<dd><p class="first last">pre-allocated numpy <tt class="docutils literal"><span class="pre">array((DIM,DIM),dtype=numpy.float32)</span></tt> which
+<dd><p class="first last">pre-allocated numpy <code class="docutils literal"><span class="pre">array((DIM,DIM),dtype=numpy.float32)</span></code> which
 is filled with the unit cell box vectors</p>
 </dd>
 <dt><em>x</em></dt>
-<dd><p class="first last">pre-allocated numpy <tt class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></tt>
+<dd><p class="first last">pre-allocated numpy <code class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></code>
 which is updated with the <strong>coordinates</strong> from the frame</p>
 </dd>
 <dt><em>v</em></dt>
-<dd><p class="first last">pre-allocated numpy <tt class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></tt>
+<dd><p class="first last">pre-allocated numpy <code class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></code>
 which is updated with the <strong>velocities</strong> from the frame</p>
 </dd>
 <dt><em>f</em></dt>
-<dd><p class="first last">pre-allocated numpy <tt class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></tt>
+<dd><p class="first last">pre-allocated numpy <code class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></code>
 which is updated with the <strong>forces</strong> from the frame</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt>a tuple containing:</dt>
 <dd><dl class="first last docutils">
 <dt><em>status</em></dt>
-<dd><p class="first last">integer status (0 = exdrOK), see the <tt class="docutils literal"><span class="pre">libxdrfile2.exdr*</span></tt> constants 
+<dd><p class="first last">integer status (0 = exdrOK), see the <code class="docutils literal"><span class="pre">libxdrfile2.exdr*</span></code> constants 
 under <a class="reference internal" href="#status-symbols">Status symbols</a> for other values)</p>
 </dd>
 <dt><em>step</em></dt>
@@ -604,13 +605,13 @@ <h3>5.21.4.2.4. TRR functions<a class="headerlink" href="#trr-functions" title="
 
 <dl class="function">
 <dt id="MDAnalysis.coordinates.xdrfile.libxdrfile2.write_trr">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</tt><tt class="descname">write_trr</tt><big>(</big><em>XDRFILE</em>, <em>step</em>, <em>time</em>, <em>lambda</em>, <em>box</em>, <em>x</em>, <em>v</em>, <em>f</em><big>)</big> &rarr; status<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#write_trr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.write_trr" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.libxdrfile2.</code><code class="descname">write_trr</code><span class="sig-paren">(</span><em>XDRFILE</em>, <em>step</em>, <em>time</em>, <em>lambda</em>, <em>box</em>, <em>x</em>, <em>v</em>, <em>f</em><span class="sig-paren">)</span> &rarr; status<a class="reference internal" href="../../../_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html#write_trr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.libxdrfile2.write_trr" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write the next frame to the opened trr trajectory.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>XDRFILE</em></dt>
 <dd><p class="first last">open <em>XDRFILE</em> object (writable)</p>
 </dd>
@@ -624,19 +625,19 @@ <h3>5.21.4.2.4. TRR functions<a class="headerlink" href="#trr-functions" title="
 <dd><p class="first last">free energy lambda value (typically 0.0)</p>
 </dd>
 <dt><em>box</em></dt>
-<dd><p class="first last">numpy <tt class="docutils literal"><span class="pre">array((DIM,DIM),dtype=numpy.float32)</span></tt> which contains 
+<dd><p class="first last">numpy <code class="docutils literal"><span class="pre">array((DIM,DIM),dtype=numpy.float32)</span></code> which contains 
 the unit cell box vectors</p>
 </dd>
 <dt><em>x</em></dt>
-<dd><p class="first last">numpy <tt class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></tt>
+<dd><p class="first last">numpy <code class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></code>
 which contains the <strong>coordinates</strong> from the frame</p>
 </dd>
 <dt><em>v</em></dt>
-<dd><p class="first last">numpy <tt class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></tt>
+<dd><p class="first last">numpy <code class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></code>
 which contains the <strong>velocities</strong> from the frame</p>
 </dd>
 <dt><em>f</em></dt>
-<dd><p class="first last">numpy <tt class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></tt>
+<dd><p class="first last">numpy <code class="docutils literal"><span class="pre">array((natoms,</span> <span class="pre">DIM),dtype=nump.float32)</span></code>
 which contains the <strong>forces</strong> from the frame</p>
 </dd>
 </dl>
@@ -644,15 +645,16 @@ <h3>5.21.4.2.4. TRR functions<a class="headerlink" href="#trr-functions" title="
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.0: </span>either one of <em>x</em>, <em>v</em>, or <em>f</em> can now be set as a natom,0-DIM
-numpy <tt class="docutils literal"><span class="pre">array((natom,</span> <span class="pre">0),dtype=nump.float32)</span></tt>. This will cause the
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.0: </span>either one of <em>x</em>, <em>v</em>, or <em>f</em> can now be set as a natom,0-DIM
+numpy <code class="docutils literal"><span class="pre">array((natom,</span> <span class="pre">0),dtype=nump.float32)</span></code>. This will cause the
 corresponding property to be skipped when writing to file.</p>
+</div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><em>status</em>, integer status (0 = OK), see the <tt class="docutils literal"><span class="pre">libxdrfile2.exdr*</span></tt> 
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><em>status</em>, integer status (0 = OK), see the <code class="docutils literal"><span class="pre">libxdrfile2.exdr*</span></code> 
 constants under <a class="reference internal" href="#status-symbols">Status symbols</a> for other values)</td>
 </tr>
 </tbody>
@@ -669,7 +671,7 @@ <h3>5.21.4.2.4. TRR functions<a class="headerlink" href="#trr-functions" title="
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -684,12 +686,12 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="core.html" title="5.21.3. Common high-level Gromacs XDR functionality — MDAnalysis.coordinates.xdrfile.core"
              >previous</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
-          <li><a href="../xdrfile.html" >5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
+          <li class="nav-item nav-item-2"><a href="../xdrfile.html" >5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -699,7 +701,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile/statno.html b/package/doc/html/documentation_pages/coordinates/xdrfile/statno.html
index 0e76a991b58..4568ad76dd2 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile/statno.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile/statno.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5.21.5. Status codes and symbols — statno &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5.21.5. Status codes and symbols — statno &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../../index.html" />
     <link rel="up" title="5.21. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile" href="../xdrfile.html" />
     <link rel="next" title="5.22. Extensions to Bio.PDB — pdb.extensions" href="../pdbextensions.html" />
     <link rel="prev" title="5.21.4. The Gromacs XTC/TRR library libxdrfile2" href="libxdrfile2.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,28 +49,30 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="libxdrfile2.html" title="5.21.4. The Gromacs XTC/TRR library libxdrfile2"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
-          <li><a href="../xdrfile.html" accesskey="U">5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
+          <li class="nav-item nav-item-2"><a href="../xdrfile.html" accesskey="U">5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../../index.html">
               <img class="logo" src="../../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="libxdrfile2.html"
-                        title="previous chapter">5.21.4. The Gromacs XTC/TRR library <tt class="docutils literal docutils literal docutils literal"><span class="pre">libxdrfile2</span></tt></a></p>
+                        title="previous chapter">5.21.4. The Gromacs XTC/TRR library <code class="docutils literal"><span class="pre">libxdrfile2</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="../pdbextensions.html"
-                        title="next chapter">5.22. Extensions to <tt class="docutils literal docutils literal"><span class="pre">Bio.PDB</span></tt> &#8212; <tt class="docutils literal docutils literal"><span class="pre">pdb.extensions</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../../_sources/documentation_pages/coordinates/xdrfile/statno.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.22. Extensions to <code class="docutils literal"><span class="pre">Bio.PDB</span></code> &#8212; <code class="docutils literal"><span class="pre">pdb.extensions</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../../_sources/documentation_pages/coordinates/xdrfile/statno.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../../search.html" method="get">
       <input type="text" name="q" />
@@ -91,24 +91,24 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.coordinates.xdrfile.statno"></span><div class="section" id="status-codes-and-symbols-statno">
-<h1>5.21.5. Status codes and symbols &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.xdrfile.statno" title="MDAnalysis.coordinates.xdrfile.statno"><tt class="xref py py-mod docutils literal"><span class="pre">statno</span></tt></a><a class="headerlink" href="#status-codes-and-symbols-statno" title="Permalink to this headline">¶</a></h1>
+<h1>5.21.5. Status codes and symbols &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.xdrfile.statno" title="MDAnalysis.coordinates.xdrfile.statno"><code class="xref py py-mod docutils literal"><span class="pre">statno</span></code></a><a class="headerlink" href="#status-codes-and-symbols-statno" title="Permalink to this headline">¶</a></h1>
 <p>The module makes all the status symbols available that are used in
-<a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></tt></a> (and which are
+<a class="reference internal" href="libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2" title="MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref py py-mod docutils literal"><span class="pre">libxdrfile2</span></code></a> (and which are
 described there). The value of each symbol is an integer (as defined
-in <tt class="docutils literal"><span class="pre">xdrfile.h</span></tt>).</p>
-<p>The dictionary <tt class="xref py py-data docutils literal"><span class="pre">xdrfile.errno.errorcode</span></tt> maps numeric codes to
+in <code class="docutils literal"><span class="pre">xdrfile.h</span></code>).</p>
+<p>The dictionary <code class="xref py py-data docutils literal"><span class="pre">xdrfile.errno.errorcode</span></code> maps numeric codes to
 symbol names.</p>
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.statno.ERRORCODE">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.statno.</tt><tt class="descname">ERRORCODE</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.statno.ERRORCODE" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.statno.</code><code class="descname">ERRORCODE</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.statno.ERRORCODE" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.coordinates.xdrfile.statno.ERRORSYMBOLS">
-<tt class="descclassname">MDAnalysis.coordinates.xdrfile.statno.</tt><tt class="descname">ERRORSYMBOLS</tt><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.statno.ERRORSYMBOLS" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.coordinates.xdrfile.statno.</code><code class="descname">ERRORSYMBOLS</code><a class="headerlink" href="#MDAnalysis.coordinates.xdrfile.statno.ERRORSYMBOLS" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 </div>
@@ -119,7 +119,7 @@ <h1>5.21.5. Status codes and symbols &#8212; <a class="reference internal" href=
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -134,12 +134,12 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="libxdrfile2.html" title="5.21.4. The Gromacs XTC/TRR library libxdrfile2"
              >previous</a> |</li>
-        <li><a href="../../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
-          <li><a href="../xdrfile.html" >5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../../coordinates_modules.html" >5. Coordinates modules</a> &raquo;</li>
+          <li class="nav-item nav-item-2"><a href="../xdrfile.html" >5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -149,7 +149,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates_modules.html b/package/doc/html/documentation_pages/coordinates_modules.html
index 312e8703599..83e4e6ec6a1 100644
--- a/package/doc/html/documentation_pages/coordinates_modules.html
+++ b/package/doc/html/documentation_pages/coordinates_modules.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>5. Coordinates modules &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>5. Coordinates modules &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="5.1. Trajectory Readers and Writers — MDAnalysis.coordinates" href="coordinates/init.html" />
-    <link rel="prev" title="4.21. Utility functions for the TPR topology parser" href="topology/tpr_util.html" /> 
+    <link rel="prev" title="4.22. Utility functions for the TPR topology parser" href="topology/tpr_util.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -48,28 +46,30 @@ <h3>Navigation</h3>
           <a href="coordinates/init.html" title="5.1. Trajectory Readers and Writers — MDAnalysis.coordinates"
              accesskey="N">next</a> |</li>
         <li class="right" >
-          <a href="topology/tpr_util.html" title="4.21. Utility functions for the TPR topology parser"
+          <a href="topology/tpr_util.html" title="4.22. Utility functions for the TPR topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
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               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="topology/tpr_util.html"
-                        title="previous chapter">4.21. Utility functions for the TPR topology parser</a></p>
+                        title="previous chapter">4.22. Utility functions for the TPR topology parser</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="coordinates/init.html"
-                        title="next chapter">5.1. Trajectory Readers and Writers  &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/coordinates_modules.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">5.1. Trajectory Readers and Writers  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/coordinates_modules.txt"
+            rel="nofollow">Show Source</a></li>
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+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -88,49 +88,49 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="coordinates-modules">
 <span id="coordinates"></span><h1>5. Coordinates modules<a class="headerlink" href="#coordinates-modules" title="Permalink to this headline">¶</a></h1>
 <p>The coordinates module contains the classes to read and write
-trajectories. Typically, MDAnalysis recognizes <a class="reference internal" href="coordinates/init.html#id1"><em>Table of supported coordinate formats</em></a> by the file extension and hence most users probably do not need to
+trajectories. Typically, MDAnalysis recognizes <a class="reference internal" href="coordinates/init.html#id1"><span>Table of supported coordinate formats</span></a> by the file extension and hence most users probably do not need to
 concern themselves with classes and functions described here. However,
 if MDAnalysis fails to recognize a coordinate file then the user can
 provide the format in the keyword argument <em>format</em> to
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> to force the format.</p>
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> to force the format.</p>
 <p class="rubric">Coordinate formats</p>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/init.html">5.1. Trajectory Readers and Writers  &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/CRD.html">5.2. CRD structure files in MDAnalysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.CRD</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/DCD.html">5.3. DCD trajectory I/O  &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/DLPoly.html">5.4. DL_Poly format reader <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.DLPoly</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/DMS.html">5.5. DESRES file format &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.DMS</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/GMS.html">5.6. GAMESS trajectory reader &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.GMS</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/GRO.html">5.7. GRO file format &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/INPCRD.html">5.8. INPCRD structure files in MDAnalysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.INPCRD</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/LAMMPS.html">5.9. LAMMPS DCD trajectory I/O  &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/MOL2.html">5.10. MOL2 file format &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/PDB.html">5.11. PDB structure files in MDAnalysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/PDBQT.html">5.12. PDBQT structure files in MDAnalysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.PDBQT</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/PQR.html">5.13. PQR file format &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.PQR</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/TRJ.html">5.14. AMBER trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/TRR.html">5.15. Gromacs TRR file IO &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRR</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/XTC.html">5.16. Gromacs XTC file IO &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/XYZ.html">5.17. XYZ trajectory reader &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.XYZ</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/TRZ.html">5.18. TRZ trajectory I/O  &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRZ</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/init.html">5.1. Trajectory Readers and Writers  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/CRD.html">5.2. CRD structure files in MDAnalysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.CRD</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/DCD.html">5.3. DCD trajectory I/O  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.DCD</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/DLPoly.html">5.4. DL_Poly format reader <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.DLPoly</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/DMS.html">5.5. DESRES file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.DMS</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/GMS.html">5.6. GAMESS trajectory reader &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.GMS</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/GRO.html">5.7. GRO file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/INPCRD.html">5.8. INPCRD structure files in MDAnalysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.INPCRD</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/LAMMPS.html">5.9. LAMMPS DCD trajectory I/O  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/MOL2.html">5.10. MOL2 file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/PDB.html">5.11. PDB structure files in MDAnalysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/PDBQT.html">5.12. PDBQT structure files in MDAnalysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.PDBQT</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/PQR.html">5.13. PQR file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.PQR</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/TRJ.html">5.14. AMBER trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRJ</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/TRR.html">5.15. Gromacs TRR file IO &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRR</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/XTC.html">5.16. Gromacs XTC file IO &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.XTC</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/XYZ.html">5.17. XYZ trajectory reader &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.XYZ</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/TRZ.html">5.18. TRZ trajectory I/O  &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.TRZ</span></code></a></li>
 </ul>
 </div>
 <p class="rubric">Coordinate core modules</p>
 <p>The remaining pages are primarily of interest to
 developers. Programmers and anyone trying to implement new
-functionality should first read the <a class="reference internal" href="coordinates/init.html#trajectory-api"><em>Trajectory API</em></a>.</p>
+functionality should first read the <a class="reference internal" href="coordinates/init.html#trajectory-api"><span>Trajectory API</span></a>.</p>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/base.html">5.19. Base classes &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/core.html">5.20. Common functions for coordinate reading &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.core</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/xdrfile.html">5.21. NumPy access to Gromacs XDR trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="coordinates/pdbextensions.html">5.22. Extensions to <tt class="docutils literal"><span class="pre">Bio.PDB</span></tt> &#8212; <tt class="docutils literal"><span class="pre">pdb.extensions</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/base.html">5.19. Base classes &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.base</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/core.html">5.20. Common functions for coordinate reading &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.core</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/xdrfile.html">5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.xdrfile</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="coordinates/pdbextensions.html">5.22. Extensions to <code class="docutils literal"><span class="pre">Bio.PDB</span></code> &#8212; <code class="docutils literal"><span class="pre">pdb.extensions</span></code></a></li>
 </ul>
 </div>
 </div>
@@ -141,7 +141,7 @@ <h3>Quick search</h3>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -154,12 +154,12 @@ <h3>Navigation</h3>
           <a href="coordinates/init.html" title="5.1. Trajectory Readers and Writers — MDAnalysis.coordinates"
              >next</a> |</li>
         <li class="right" >
-          <a href="topology/tpr_util.html" title="4.21. Utility functions for the TPR topology parser"
+          <a href="topology/tpr_util.html" title="4.22. Utility functions for the TPR topology parser"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
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-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
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@@ -169,7 +169,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/AtomGroup.html b/package/doc/html/documentation_pages/core/AtomGroup.html
index 2e208341647..49e30c6faa6 100644
--- a/package/doc/html/documentation_pages/core/AtomGroup.html
+++ b/package/doc/html/documentation_pages/core/AtomGroup.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>7.2. Fundamental building blocks — MDAnalysis.core.AtomGroup &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>7.2. Fundamental building blocks — MDAnalysis.core.AtomGroup &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="7. Core modules" href="../core_modules.html" />
     <link rel="next" title="7.3. Atom selection Hierarchy — MDAnalysis.core.Selection" href="Selection.html" />
     <link rel="prev" title="7.1. Core functions of MDAnalysis" href="init.html" /> 
   </head>
-  <body>
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="init.html" title="7.1. Core functions of MDAnalysis"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../core_modules.html" accesskey="U">7. Core modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../core_modules.html" accesskey="U">7. Core modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">7.2. Fundamental building blocks &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></tt></a><ul>
+<li><a class="reference internal" href="#">7.2. Fundamental building blocks &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></code></a><ul>
 <li><a class="reference internal" href="#class-hierarchy">7.2.1. Class Hierarchy</a></li>
 <li><a class="reference internal" href="#manipulating-atoms-residues-and-segments">7.2.2. Manipulating atoms, residues, and segments</a></li>
 <li><a class="reference internal" href="#working-with-topologies">7.2.3. Working with Topologies</a></li>
@@ -81,13 +79,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">7.1. Core functions of MDAnalysis</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="Selection.html"
-                        title="next chapter">7.3. Atom selection Hierarchy &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.core.Selection</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/core/AtomGroup.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">7.3. Atom selection Hierarchy &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.Selection</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/core/AtomGroup.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
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@@ -106,27 +106,27 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
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-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.core.AtomGroup"></span><div class="section" id="fundamental-building-blocks-mdanalysis-core-atomgroup">
-<h1>7.2. Fundamental building blocks &#8212; <a class="reference internal" href="#module-MDAnalysis.core.AtomGroup" title="MDAnalysis.core.AtomGroup"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></tt></a><a class="headerlink" href="#fundamental-building-blocks-mdanalysis-core-atomgroup" title="Permalink to this headline">¶</a></h1>
+<h1>7.2. Fundamental building blocks &#8212; <a class="reference internal" href="#module-MDAnalysis.core.AtomGroup" title="MDAnalysis.core.AtomGroup"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></code></a><a class="headerlink" href="#fundamental-building-blocks-mdanalysis-core-atomgroup" title="Permalink to this headline">¶</a></h1>
 <p>The most important data structure in MDAnalysis is the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>, which contains <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances.</p>
-<p>A <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> is the user-visible entry point and collects all
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>, which contains <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances.</p>
+<p>A <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> is the user-visible entry point and collects all
 information needed to analyze a structure or a whole trajectory.</p>
 <p>Segments and residues are a way to refer to a collection of atoms. By
-convention, a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> is a single amino acid, or a water
-molecule, ion, or ligand. A <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a> is a collection of
+convention, a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> is a single amino acid, or a water
+molecule, ion, or ligand. A <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></a> is a collection of
 residues such as a whole protein or a chain in a protein or all the
 water in the system.</p>
 <div class="section" id="class-hierarchy">
 <h2>7.2.1. Class Hierarchy<a class="headerlink" href="#class-hierarchy" title="Permalink to this headline">¶</a></h2>
-<p>A <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> contains Segments, which contain Residues, which
-contain Atoms; all containers are derived from <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>, and
+<p>A <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> contains Segments, which contain Residues, which
+contain Atoms; all containers are derived from <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>, and
 thus one can always analyze them as a collection of atoms, independent
 of the hierarchical level.</p>
-<p>Each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> can only belong to a single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a>, and a
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> belongs to one specific <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a>. This
+<p>Each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> can only belong to a single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a>, and a
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> belongs to one specific <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></a>. This
 hierarchy can be described as</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">Segment</span> <span class="o">&gt;</span> <span class="n">Residue</span> <span class="o">&gt;</span> <span class="n">Atom</span>
 </pre></div>
@@ -135,24 +135,24 @@ <h2>7.2.1. Class Hierarchy<a class="headerlink" href="#class-hierarchy" title="P
 on, for instance, the basis of residues than atoms, or to write out
 individual chains (segments) of a protein. MDAnalysis simply provides
 access to these groupings and keeps track of where an atom
-belongs. Each object provides three attributes (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.atoms"><tt class="xref py py-attr docutils literal"><span class="pre">atoms</span></tt></a>,
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="MDAnalysis.core.AtomGroup.AtomGroup.residues"><tt class="xref py py-attr docutils literal"><span class="pre">residues</span></tt></a> or <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.residue" title="MDAnalysis.core.AtomGroup.Atom.residue"><tt class="xref py py-attr docutils literal"><span class="pre">residue</span></tt></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.segments" title="MDAnalysis.core.AtomGroup.AtomGroup.segments"><tt class="xref py py-attr docutils literal"><span class="pre">segments</span></tt></a> or
-<tt class="xref py py-attr docutils literal"><span class="pre">segment</span></tt>) that give access to the tiers in the hierarchy
+belongs. Each object provides three attributes (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.atoms"><code class="xref py py-attr docutils literal"><span class="pre">atoms</span></code></a>,
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="MDAnalysis.core.AtomGroup.AtomGroup.residues"><code class="xref py py-attr docutils literal"><span class="pre">residues</span></code></a> or <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.residue" title="MDAnalysis.core.AtomGroup.Atom.residue"><code class="xref py py-attr docutils literal"><span class="pre">residue</span></code></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.segments" title="MDAnalysis.core.AtomGroup.AtomGroup.segments"><code class="xref py py-attr docutils literal"><span class="pre">segments</span></code></a> or
+<code class="xref py py-attr docutils literal"><span class="pre">segment</span></code>) that give access to the tiers in the hierarchy
 that the object belongs to.</p>
 </div>
 <div class="section" id="manipulating-atoms-residues-and-segments">
 <h2>7.2.2. Manipulating atoms, residues, and segments<a class="headerlink" href="#manipulating-atoms-residues-and-segments" title="Permalink to this headline">¶</a></h2>
 <p>When working with MDAnalysis it is useful to remember that the fundamental
-object is the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>. Each particle in the topology is represented by
-exactly one <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instance. One <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>, however, can be a member
-of multiple <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> collections, for instance from different
-selections even though they all refer to the <em>same</em> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> object. Thus,
-changing a property of a specific and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> in one <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
+object is the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>. Each particle in the topology is represented by
+exactly one <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instance. One <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>, however, can be a member
+of multiple <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> collections, for instance from different
+selections even though they all refer to the <em>same</em> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> object. Thus,
+changing a property of a specific and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> in one <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
 changes it &#8220;everywhere&#8221;.</p>
-<p>The same is mostly true for <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> instances although they are
-derived from <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances: all <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> objects with the same
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="MDAnalysis.core.AtomGroup.Atom.resid"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.resid</span></tt></a> are bundled into a single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> with
-<tt class="xref py py-class docutils literal"><span class="pre">Residue.id</span></tt> = <em>resid</em>. This means that just changing, say, the residue
+<p>The same is mostly true for <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> instances although they are
+derived from <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances: all <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> objects with the same
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="MDAnalysis.core.AtomGroup.Atom.resid"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resid</span></code></a> are bundled into a single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> with
+<code class="xref py py-class docutils literal"><span class="pre">Residue.id</span></code> = <em>resid</em>. This means that just changing, say, the residue
 name with a command such as</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">r</span> <span class="o">=</span> <span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;resid 99&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="k">print</span><span class="p">(</span><span class="n">r</span><span class="p">)</span>
@@ -166,31 +166,34 @@ <h2>7.2.2. Manipulating atoms, residues, and segments<a class="headerlink" href=
 </pre></div>
 </div>
 <p>will typically work as expected. When working with collections such as
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> or <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a> it is generally better to use
-provided setter methods such as <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resname" title="MDAnalysis.core.AtomGroup.AtomGroup.set_resname"><tt class="xref py py-meth docutils literal"><span class="pre">AtomGroup.set_resname()</span></tt></a> or
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resname" title="MDAnalysis.core.AtomGroup.ResidueGroup.set_resname"><tt class="xref py py-meth docutils literal"><span class="pre">ResidueGroup.set_resname()</span></tt></a>.</p>
-<p>There are two cases when it is very important to use the setters:</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> or <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a> it is generally better to use
+properties such as <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.resnames" title="MDAnalysis.core.AtomGroup.AtomGroup.resnames"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.resnames</span></code></a> or <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup.resnames" title="MDAnalysis.core.AtomGroup.ResidueGroup.resnames"><code class="xref py py-attr docutils literal"><span class="pre">ResidueGroup.resnames</span></code></a>
+to modify their items&#8217; attributes.</p>
+<p>There are two cases when it is very important to use these collective
+properties:</p>
 <ul class="simple">
-<li>changing <em>resid</em>: <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resid" title="MDAnalysis.core.AtomGroup.AtomGroup.set_resid"><tt class="xref py py-meth docutils literal"><span class="pre">AtomGroup.set_resid()</span></tt></a> and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resid" title="MDAnalysis.core.AtomGroup.ResidueGroup.set_resid"><tt class="xref py py-meth docutils literal"><span class="pre">ResidueGroup.set_resid()</span></tt></a></li>
-<li>changing <em>segid</em>: <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_segid" title="MDAnalysis.core.AtomGroup.AtomGroup.set_segid"><tt class="xref py py-meth docutils literal"><span class="pre">AtomGroup.set_segid()</span></tt></a> and <tt class="xref py py-meth docutils literal"><span class="pre">ResidueGroup.set_segid()</span></tt></li>
+<li>changing <em>resid</em>: <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.resids" title="MDAnalysis.core.AtomGroup.AtomGroup.resids"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.resids</span></code></a> and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup.resids" title="MDAnalysis.core.AtomGroup.ResidueGroup.resids"><code class="xref py py-attr docutils literal"><span class="pre">ResidueGroup.resids</span></code></a></li>
+<li>changing <em>segid</em>: <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.segids" title="MDAnalysis.core.AtomGroup.AtomGroup.segids"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.segids</span></code></a> and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup.segids" title="MDAnalysis.core.AtomGroup.ResidueGroup.segids"><code class="xref py py-attr docutils literal"><span class="pre">ResidueGroup.segids</span></code></a></li>
 </ul>
-<p>Because residues are determined by the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="MDAnalysis.core.AtomGroup.Atom.resid"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.resid</span></tt></a> and segments by
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.segid</span></tt></a>, the above methods take extra care to rebuild the list of
-segments and residues.</p>
+<p>Because residues are determined by the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="MDAnalysis.core.AtomGroup.Atom.resid"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resid</span></code></a> and segments by
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><code class="xref py py-attr docutils literal"><span class="pre">Atom.segid</span></code></a>, the above properties take extra care to rebuild the list of
+segments and residues. Alternatively, the same effect can be obtained using
+the corresponding setter method, e.g. <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resids" title="MDAnalysis.core.AtomGroup.AtomGroup.set_resids"><code class="xref py py-meth docutils literal"><span class="pre">AtomGroup.set_resids()</span></code></a>.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resid" title="MDAnalysis.core.AtomGroup.AtomGroup.set_resid"><tt class="xref py py-meth docutils literal"><span class="pre">AtomGroup.set_resid()</span></tt></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resid" title="MDAnalysis.core.AtomGroup.ResidueGroup.set_resid"><tt class="xref py py-meth docutils literal"><span class="pre">ResidueGroup.set_resid()</span></tt></a>,
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_segid" title="MDAnalysis.core.AtomGroup.AtomGroup.set_segid"><tt class="xref py py-meth docutils literal"><span class="pre">AtomGroup.set_segid()</span></tt></a>, <tt class="xref py py-meth docutils literal"><span class="pre">ResidueGroup.set_segid()</span></tt> can change the
-topology: they can split or merge residues or segments.</p>
+<p class="last">Setting any of
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.resids" title="MDAnalysis.core.AtomGroup.AtomGroup.resids"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.resids</span></code></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup.resids" title="MDAnalysis.core.AtomGroup.ResidueGroup.resids"><code class="xref py py-attr docutils literal"><span class="pre">ResidueGroup.resids</span></code></a>,
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.segids" title="MDAnalysis.core.AtomGroup.AtomGroup.segids"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.segids</span></code></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup.segids" title="MDAnalysis.core.AtomGroup.ResidueGroup.segids"><code class="xref py py-attr docutils literal"><span class="pre">ResidueGroup.segids</span></code></a> 
+can change the topology: they can split or merge residues or segments.</p>
 </div>
 <p>Splitting/merging of residues is probably not very useful because no chemical
 rearrangements are carried out. Manipulating segments might be more useful in
-order to add additional structure to a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> and provide instant
+order to add additional structure to a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> and provide instant
 segment selectors for interactive work:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;protein&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">set_segid</span><span class="p">(</span><span class="s">&quot;protein&quot;</span><span class="p">)</span>
-<span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;resname POPE or resname POPC&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">set_segid</span><span class="p">(</span><span class="s">&quot;lipids&quot;</span><span class="p">)</span>
-<span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;resname SOL&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">set_segid</span><span class="p">(</span><span class="s">&quot;water&quot;</span><span class="p">)</span>
-<span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;resname NA or resname CL&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">set_segid</span><span class="p">(</span><span class="s">&quot;ions&quot;</span><span class="p">)</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;protein&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">set_segids</span><span class="p">(</span><span class="s">&quot;protein&quot;</span><span class="p">)</span>
+<span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;resname POPE or resname POPC&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">set_segids</span><span class="p">(</span><span class="s">&quot;lipids&quot;</span><span class="p">)</span>
+<span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;resname SOL&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">set_segids</span><span class="p">(</span><span class="s">&quot;water&quot;</span><span class="p">)</span>
+<span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;resname NA or resname CL&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">set_segids</span><span class="p">(</span><span class="s">&quot;ions&quot;</span><span class="p">)</span>
 
 <span class="n">u</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">n_residues</span>
 <span class="n">water_oxygens</span> <span class="o">=</span> <span class="n">u</span><span class="o">.</span><span class="n">water</span><span class="o">.</span><span class="n">OW</span>
@@ -202,27 +205,27 @@ <h2>7.2.2. Manipulating atoms, residues, and segments<a class="headerlink" href=
 N-terminus. Let&#8217;s say that the first residue is really residue 10. In order to
 store the canonical residue IDs (&#8220;resnum&#8221;) one could the use</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">protein</span> <span class="o">=</span> <span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;protein&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">residues</span>
-<span class="n">protein</span><span class="o">.</span><span class="n">set_resnum</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">resnums</span> <span class="o">+</span> <span class="mi">9</span><span class="p">)</span>
+<span class="n">protein</span><span class="o">.</span><span class="n">set_resnums</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">resnums</span> <span class="o">+</span> <span class="mi">9</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>One can then use <tt class="docutils literal"><span class="pre">protein.select(&quot;resnum</span> <span class="pre">42&quot;)</span></tt> to select the residue that has
-the canonical residue id 42 (instead of <tt class="docutils literal"><span class="pre">resid</span> <span class="pre">33</span></tt>).</p>
-<p>One can also read the resids directly from  an original PDB file:</p>
+<p>One can then use <code class="docutils literal"><span class="pre">protein.select(&quot;resnum</span> <span class="pre">42&quot;)</span></code> to select the residue that has
+the canonical residue id 42 (instead of <code class="docutils literal"><span class="pre">resid</span> <span class="pre">33</span></code>).</p>
+<p>One can also read the resids directly from an original PDB file:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">orig</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="s">&quot;2jln.pdb&quot;</span><span class="p">)</span>
-<span class="n">protein</span><span class="o">.</span><span class="n">set_resnum</span><span class="p">(</span><span class="n">orig</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;protein&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">resids</span><span class="p">)</span>
+<span class="n">protein</span><span class="o">.</span><span class="n">set_resnums</span><span class="p">(</span><span class="n">orig</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;protein&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">resids</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
 <div class="section" id="working-with-topologies">
 <h2>7.2.3. Working with Topologies<a class="headerlink" href="#working-with-topologies" title="Permalink to this headline">¶</a></h2>
 <p>If the topology file given to the Universe had bonding information then this
-will have been loaded into the Universe as <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.bonds" title="MDAnalysis.core.AtomGroup.Universe.bonds"><tt class="xref py py-attr docutils literal"><span class="pre">Universe.bonds</span></tt></a>
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.angles" title="MDAnalysis.core.AtomGroup.Universe.angles"><tt class="xref py py-attr docutils literal"><span class="pre">Universe.angles</span></tt></a> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.dihedrals" title="MDAnalysis.core.AtomGroup.Universe.dihedrals"><tt class="xref py py-attr docutils literal"><span class="pre">Universe.dihedrals</span></tt></a> and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.impropers" title="MDAnalysis.core.AtomGroup.Universe.impropers"><tt class="xref py py-attr docutils literal"><span class="pre">Universe.impropers</span></tt></a>.</p>
+will have been loaded into the Universe as <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.bonds" title="MDAnalysis.core.AtomGroup.Universe.bonds"><code class="xref py py-attr docutils literal"><span class="pre">Universe.bonds</span></code></a>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.angles" title="MDAnalysis.core.AtomGroup.Universe.angles"><code class="xref py py-attr docutils literal"><span class="pre">Universe.angles</span></code></a> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.dihedrals" title="MDAnalysis.core.AtomGroup.Universe.dihedrals"><code class="xref py py-attr docutils literal"><span class="pre">Universe.dihedrals</span></code></a> and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.impropers" title="MDAnalysis.core.AtomGroup.Universe.impropers"><code class="xref py py-attr docutils literal"><span class="pre">Universe.impropers</span></code></a>.</p>
 <p>If your topology file does not have this information, it is still possible
 to construct it based on the positions of the atoms and assumed vdw radii
-for these atoms.  See <tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.AtomGroup.guess_bonds()</span></tt> and
-<a class="reference internal" href="../topology/core.html#MDAnalysis.topology.core.guess_bonds" title="MDAnalysis.topology.core.guess_bonds"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.core.guess_bonds()</span></tt></a> for details.</p>
-<p>This Topology information is stored in <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.TopologyGroup</span></tt>
+for these atoms.  See <code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.AtomGroup.guess_bonds()</span></code> and
+<a class="reference internal" href="../topology/core.html#MDAnalysis.topology.core.guess_bonds" title="MDAnalysis.topology.core.guess_bonds"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.core.guess_bonds()</span></code></a> for details.</p>
+<p>This Topology information is stored in <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.TopologyGroup</span></code>
 objects.  These are designed to be analogous to the AtomGroup container for Atoms.</p>
 <p>For examples working with a box of ethanol:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">MDAnalysis</span> <span class="kn">as</span> <span class="nn">mda</span>
@@ -246,10 +249,11 @@ <h2>7.2.3. Working with Topologies<a class="headerlink" href="#working-with-topo
 <span class="go"> (&#39;H&#39;, &#39;C&#39;, &#39;O&#39;)]</span>
 </pre></div>
 </div>
-<p>There is only C-C-H bonds and no H-C-C bonds.  Selection however is
+<p>There are only C-C-H bonds and no H-C-C bonds.  Selection however is
 aware that sometimes types are reversed:</p>
-<div class="highlight-python"><pre>u.angles.select_bonds(('H', 'C', 'C'))  # note reversal of type
-&gt;&gt;&gt; &lt;TopologyGroup containing 7365 Angles&gt;</pre>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">u</span><span class="o">.</span><span class="n">angles</span><span class="o">.</span><span class="n">select_bonds</span><span class="p">((</span><span class="s">&#39;H&#39;</span><span class="p">,</span> <span class="s">&#39;C&#39;</span><span class="p">,</span> <span class="s">&#39;C&#39;</span><span class="p">))</span>  <span class="c"># note reversal of type</span>
+<span class="go">&lt;TopologyGroup containing 7365 Angles&gt;</span>
+</pre></div>
 </div>
 <p>TopologyGroups can be combined and indexed:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">tg</span> <span class="o">=</span> <span class="n">u</span><span class="o">.</span><span class="n">angles</span><span class="o">.</span><span class="n">select_bonds</span><span class="p">((</span><span class="s">&#39;C&#39;</span><span class="p">,</span> <span class="s">&#39;C&#39;</span><span class="p">,</span> <span class="s">&#39;O&#39;</span><span class="p">))</span> <span class="o">+</span> <span class="n">u</span><span class="o">.</span><span class="n">angles</span><span class="o">.</span><span class="n">select_bonds</span><span class="p">((</span><span class="s">&#39;C&#39;</span><span class="p">,</span> <span class="s">&#39;O&#39;</span><span class="p">,</span> <span class="s">&#39;H&#39;</span><span class="p">))</span>
@@ -270,16 +274,16 @@ <h2>7.2.3. Working with Topologies<a class="headerlink" href="#working-with-topo
 <div class="section" id="combining-objects-system-building">
 <h2>7.2.4. Combining objects: system building<a class="headerlink" href="#combining-objects-system-building" title="Permalink to this headline">¶</a></h2>
 <p>It is often convenient to combined multiple groups of atoms into a single
-object. If they are contained in a single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> then the methods
+object. If they are contained in a single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> then the methods
 described above (especially manipulating the segments) might be
-useful. However, if the atoms reside in different universes, the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Merge" title="MDAnalysis.core.AtomGroup.Merge"><tt class="xref py py-func docutils literal"><span class="pre">Merge()</span></tt></a>
+useful. However, if the atoms reside in different universes, the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Merge" title="MDAnalysis.core.AtomGroup.Merge"><code class="xref py py-func docutils literal"><span class="pre">Merge()</span></code></a>
 function can be used.</p>
 <div class="section" id="merging">
 <h3>7.2.4.1. Merging<a class="headerlink" href="#merging" title="Permalink to this headline">¶</a></h3>
-<p>In the following example for <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Merge" title="MDAnalysis.core.AtomGroup.Merge"><tt class="xref py py-func docutils literal"><span class="pre">Merge()</span></tt></a>, protein, ligand, and solvent were
+<p>In the following example for <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Merge" title="MDAnalysis.core.AtomGroup.Merge"><code class="xref py py-func docutils literal"><span class="pre">Merge()</span></code></a>, protein, ligand, and solvent were
 externally prepared in three different PDB files. They are loaded into separate
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> objects (where they could be further manipulated,
-e.g. renumbered, relabeled, rotated, ...) The <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Merge" title="MDAnalysis.core.AtomGroup.Merge"><tt class="xref py py-func docutils literal"><span class="pre">Merge()</span></tt></a> command is used to
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> objects (where they could be further manipulated,
+e.g. renumbered, relabeled, rotated, ...) The <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Merge" title="MDAnalysis.core.AtomGroup.Merge"><code class="xref py py-func docutils literal"><span class="pre">Merge()</span></code></a> command is used to
 combine all of them together:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">MDAnalysis</span>
 <span class="n">u1</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="s">&quot;protein.pdb&quot;</span><span class="p">)</span>
@@ -296,35 +300,36 @@ <h3>7.2.4.2. Replicating<a class="headerlink" href="#replicating" title="Permali
 <p>It is also possible to replicate a molecule to build a system with
 multiple copies of the same molecule. In the example, we replicate an
 AdK molecule and then translate and rotate the second copy:</p>
-<div class="highlight-python"><pre>import MDAnalysis; from MDAnalysis.tests.datafiles import *
+<div class="highlight-python"><div class="highlight"><pre>import MDAnalysis; from MDAnalysis.tests.datafiles import *
 u = MDAnalysis.Universe(PSF, DCD)
-p = u.select_atoms("protein")
+p = u.select_atoms(&quot;protein&quot;)
 m = MDAnalysis.Merge(p,p)
 
 # now renumber resids and segids for each copy
 
-# first copy of the protein (need to use atom indices because currently that's the only reliable property in the
+# first copy of the protein (need to use atom indices because currently that&#39;s the only reliable property in the
 merged universe)
-p1 = m.select_atoms("bynum 1:3341")
+p1 = m.select_atoms(&quot;bynum 1:3341&quot;)
 # second copy
-p2 = m.select_atoms("bynum 3342:6682")
+p2 = m.select_atoms(&quot;bynum 3342:6682&quot;)
 
-p1.set_segid("A")
-p2.set_segid("B")
+p1.set_segid(&quot;A&quot;)
+p2.set_segid(&quot;B&quot;)
 p2.residues.set_resid(p2.residues.resids + p1.residues.resids[-1])  # increment resids for p2 with the last
 resid from p1
 
 # you must regenerate the selections after modifying them (see notes in the docs!)
 # because the changed resids are not reflected in the selection (due to how residues are referenced internally)
-p1 = m.select_atoms("segid A")       # or as before:  m.select_atoms("bynum 1:3341")
-p2 = m.select_atoms("segid B")
+p1 = m.select_atoms(&quot;segid A&quot;)       # or as before:  m.select_atoms(&quot;bynum 1:3341&quot;)
+p2 = m.select_atoms(&quot;segid B&quot;)
 
 # rotate and translate
 p2.rotateby(180, [0,0,1])
-p2.translate([50,0,0])</pre>
+p2.translate([50,0,0])
+</pre></div>
 </div>
 <p>Note that we have to manually set the residue numbers (resids) and
-segment identifies because <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Merge" title="MDAnalysis.core.AtomGroup.Merge"><tt class="xref py py-func docutils literal"><span class="pre">Merge()</span></tt></a> simply concatenates the
+segment identifies because <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Merge" title="MDAnalysis.core.AtomGroup.Merge"><code class="xref py py-func docutils literal"><span class="pre">Merge()</span></code></a> simply concatenates the
 existing atoms and only ensures that all data structures are contained
 in the new merged universe.</p>
 </div>
@@ -333,22 +338,22 @@ <h3>7.2.4.2. Replicating<a class="headerlink" href="#replicating" title="Permali
 <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functions" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.core.AtomGroup.Universe">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">Universe</tt><big>(</big><em>*args</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">Universe</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe" title="Permalink to this definition">¶</a></dt>
 <dd><p>The MDAnalysis Universe contains all the information describing the system.</p>
 <p>The system always requires a <em>topology</em> file &#8212; in the simplest case just
 a list of atoms. This can be a CHARMM/NAMD PSF file or a simple coordinate
 file with atom informations such as XYZ, PDB, Gromacs GRO, or CHARMM
-CRD. See <a class="reference internal" href="../topology/init.html#supported-topology-formats"><em>Table of Supported Topology Formats</em></a> for what kind of topologies can
+CRD. See <a class="reference internal" href="../topology/init.html#supported-topology-formats"><span>Table of Supported Topology Formats</span></a> for what kind of topologies can
 be read.</p>
 <p>A trajectory provides coordinates; the coordinates have to be ordered in
 the same way as the list of atoms in the topology. A trajectory can be a
 single frame such as a PDB, CRD, or GRO file, or it can be a MD trajectory
 (in CHARMM/NAMD/LAMMPS DCD, Gromacs XTC/TRR, or generic XYZ format).  See
-<a class="reference internal" href="../coordinates/init.html#id1"><em>Table of supported coordinate formats</em></a> for what can be read as a
+<a class="reference internal" href="../coordinates/init.html#id1"><span>Table of supported coordinate formats</span></a> for what can be read as a
 &#8220;trajectory&#8221;.</p>
 <p>As a special case, when the topology is a file that contains atom
 information <em>and</em> coordinates (such as XYZ, PDB, GRO or CRD, see
-<a class="reference internal" href="../coordinates/init.html#id1"><em>Table of supported coordinate formats</em></a>) then the coordinates are immediately
+<a class="reference internal" href="../coordinates/init.html#id1"><span>Table of supported coordinate formats</span></a>) then the coordinates are immediately
 loaded from the &#8220;topology&#8221; file unless a trajectory is supplied.</p>
 <p>Examples for setting up a universe:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">u</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">topology</span><span class="p">,</span> <span class="n">trajectory</span><span class="p">)</span>          <span class="c"># read system from file(s)</span>
@@ -362,53 +367,57 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </pre></div>
 </div>
 <p>Select atoms, with syntax similar to CHARMM (see
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><tt class="xref py py-class docutils literal"><span class="pre">select_atoms</span></tt></a> for details):</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><code class="xref py py-class docutils literal"><span class="pre">select_atoms</span></code></a> for details):</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
 </pre></div>
 </div>
 <p><em>Attributes:</em></p>
 <ul class="simple">
-<li><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.trajectory" title="MDAnalysis.core.AtomGroup.Universe.trajectory"><tt class="xref py py-attr docutils literal"><span class="pre">Universe.trajectory</span></tt></a>: currently loaded trajectory reader;
-<tt class="xref py py-attr docutils literal"><span class="pre">Universe.trajectory.ts</span></tt> is the current time step</li>
-<li><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.dimensions" title="MDAnalysis.core.AtomGroup.Universe.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">Universe.dimensions</span></tt></a>: current system dimensions (simulation unit cell, if
+<li><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.trajectory" title="MDAnalysis.core.AtomGroup.Universe.trajectory"><code class="xref py py-attr docutils literal"><span class="pre">Universe.trajectory</span></code></a>: currently loaded trajectory reader;
+<code class="xref py py-attr docutils literal"><span class="pre">Universe.trajectory.ts</span></code> is the current time step</li>
+<li><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.dimensions" title="MDAnalysis.core.AtomGroup.Universe.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">Universe.dimensions</span></code></a>: current system dimensions (simulation unit cell, if
 set in the trajectory)</li>
-<li><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.bonds" title="MDAnalysis.core.AtomGroup.Universe.bonds"><tt class="xref py py-attr docutils literal"><span class="pre">Universe.bonds</span></tt></a>: TopologyGroup of bonds in Universe, also
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.angles" title="MDAnalysis.core.AtomGroup.Universe.angles"><tt class="xref py py-attr docutils literal"><span class="pre">Universe.angles</span></tt></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.dihedrals" title="MDAnalysis.core.AtomGroup.Universe.dihedrals"><tt class="xref py py-attr docutils literal"><span class="pre">Universe.dihedrals</span></tt></a>, and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.impropers" title="MDAnalysis.core.AtomGroup.Universe.impropers"><tt class="xref py py-attr docutils literal"><span class="pre">Universe.impropers</span></tt></a>
-(low level access through <tt class="xref py py-attr docutils literal"><span class="pre">Universe._topology</span></tt>)</li>
+<li><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.bonds" title="MDAnalysis.core.AtomGroup.Universe.bonds"><code class="xref py py-attr docutils literal"><span class="pre">Universe.bonds</span></code></a>: TopologyGroup of bonds in Universe, also
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.angles" title="MDAnalysis.core.AtomGroup.Universe.angles"><code class="xref py py-attr docutils literal"><span class="pre">Universe.angles</span></code></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.dihedrals" title="MDAnalysis.core.AtomGroup.Universe.dihedrals"><code class="xref py py-attr docutils literal"><span class="pre">Universe.dihedrals</span></code></a>, and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.impropers" title="MDAnalysis.core.AtomGroup.Universe.impropers"><code class="xref py py-attr docutils literal"><span class="pre">Universe.impropers</span></code></a>
+(low level access through <code class="xref py py-attr docutils literal"><span class="pre">Universe._topology</span></code>)</li>
 </ul>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">If atom attributes such as element, mass, or charge are not explicitly
 provided in the topology file then MDAnalysis tries to guess them (see
-<a class="reference internal" href="../topology/tables.html#module-MDAnalysis.topology.tables" title="MDAnalysis.topology.tables"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tables</span></tt></a>). This does not always work and if you
+<a class="reference internal" href="../topology/tables.html#module-MDAnalysis.topology.tables" title="MDAnalysis.topology.tables"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tables</span></code></a>). This does not always work and if you
 require correct values (e.g. because you want to calculate the center of
 mass) then you need to make sure that MDAnalysis gets all the
 information needed.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Can also read multi-frame PDB files with the
-<a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></tt></a>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Parse arbitrary number of arguments as a single topology file and a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Can also read multi-frame PDB files with the
+<a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><code class="xref py py-class docutils literal"><span class="pre">PrimitivePDBReader</span></code></a>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Parse arbitrary number of arguments as a single topology file and a
 sequence of trajectories.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Topology information now loaded lazily, but can be forced with
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.build_topology" title="MDAnalysis.core.AtomGroup.Universe.build_topology"><tt class="xref py py-meth docutils literal"><span class="pre">build_topology()</span></tt></a>. Changed <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.bonds" title="MDAnalysis.core.AtomGroup.Universe.bonds"><tt class="xref py py-attr docutils literal"><span class="pre">bonds</span></tt></a> attribute to be a
-<tt class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></tt>. Added <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.angles" title="MDAnalysis.core.AtomGroup.Universe.angles"><tt class="xref py py-attr docutils literal"><span class="pre">angles</span></tt></a>
-and <tt class="xref py py-attr docutils literal"><span class="pre">torsions</span></tt> attribute as
-<tt class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></tt>. Added fragments to
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Topology information now loaded lazily, but can be forced with
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.build_topology" title="MDAnalysis.core.AtomGroup.Universe.build_topology"><code class="xref py py-meth docutils literal"><span class="pre">build_topology()</span></code></a>. Changed <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.bonds" title="MDAnalysis.core.AtomGroup.Universe.bonds"><code class="xref py py-attr docutils literal"><span class="pre">bonds</span></code></a> attribute to be a
+<code class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></code>. Added <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.angles" title="MDAnalysis.core.AtomGroup.Universe.angles"><code class="xref py py-attr docutils literal"><span class="pre">angles</span></code></a>
+and <code class="xref py py-attr docutils literal"><span class="pre">torsions</span></code> attribute as
+<code class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></code>. Added fragments to
 Universe cache</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.make_anchor" title="MDAnalysis.core.AtomGroup.Universe.make_anchor"><tt class="xref py py-meth docutils literal"><span class="pre">make_anchor()</span></tt></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.remove_anchor" title="MDAnalysis.core.AtomGroup.Universe.remove_anchor"><tt class="xref py py-meth docutils literal"><span class="pre">remove_anchor()</span></tt></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.is_anchor" title="MDAnalysis.core.AtomGroup.Universe.is_anchor"><tt class="xref py py-attr docutils literal"><span class="pre">is_anchor</span></tt></a>, and
-<tt class="xref py py-attr docutils literal"><span class="pre">anchor_name</span></tt> were added to support the pickling/unpickling of
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>.
-Deprecated <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.selectAtoms" title="MDAnalysis.core.AtomGroup.Universe.selectAtoms"><tt class="xref py py-meth docutils literal"><span class="pre">selectAtoms()</span></tt></a> in favour of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.make_anchor" title="MDAnalysis.core.AtomGroup.Universe.make_anchor"><code class="xref py py-meth docutils literal"><span class="pre">make_anchor()</span></code></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.remove_anchor" title="MDAnalysis.core.AtomGroup.Universe.remove_anchor"><code class="xref py py-meth docutils literal"><span class="pre">remove_anchor()</span></code></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.is_anchor" title="MDAnalysis.core.AtomGroup.Universe.is_anchor"><code class="xref py py-attr docutils literal"><span class="pre">is_anchor</span></code></a>, and
+<code class="xref py py-attr docutils literal"><span class="pre">anchor_name</span></code> were added to support the pickling/unpickling of
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.
+Deprecated <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.selectAtoms" title="MDAnalysis.core.AtomGroup.Universe.selectAtoms"><code class="xref py py-meth docutils literal"><span class="pre">selectAtoms()</span></code></a> in favour of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a>.</p>
+</div>
 <p>Initialize the central MDAnalysis Universe object.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>topologyfile</em></dt>
 <dd><p class="first last">A CHARMM/XPLOR PSF topology file, PDB file or Gromacs GRO file; used to define the
 list of atoms. If the file includes bond information, partial
@@ -422,29 +431,30 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 If a <strong>list of filenames</strong> is provided then they are sequentially read and appear
 as one single trajectory to the Universe. The list can contain different file
 formats.</p>
-<p class="last deprecated">
-<span class="versionmodified">Deprecated since version 0.8: </span>Do not use the <em>coordinatefile</em> keyword argument, just provide trajectories as
+<div class="last deprecated">
+<p><span class="versionmodified">Deprecated since version 0.8: </span>Do not use the <em>coordinatefile</em> keyword argument, just provide trajectories as
 positional arguments.</p>
+</div>
 </dd>
 <dt><em>permissive</em></dt>
-<dd><p class="first last">currently only relevant for PDB files: Set to <tt class="docutils literal"><span class="pre">True</span></tt> in order to ignore most errors
-and read typical MD simulation PDB files; set to <tt class="docutils literal"><span class="pre">False</span></tt> to read with the Bio.PDB reader,
-which can be useful for real Protein Databank PDB files. <tt class="docutils literal"><span class="pre">None</span></tt>  selects the
-MDAnalysis default (which is set in <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt>) [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">currently only relevant for PDB files: Set to <code class="docutils literal"><span class="pre">True</span></code> in order to ignore most errors
+and read typical MD simulation PDB files; set to <code class="docutils literal"><span class="pre">False</span></code> to read with the Bio.PDB reader,
+which can be useful for real Protein Databank PDB files. <code class="docutils literal"><span class="pre">None</span></code>  selects the
+MDAnalysis default (which is set in <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code>) [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>topology_format</em></dt>
-<dd><p class="first last">provide the file format of the topology file; <tt class="docutils literal"><span class="pre">None</span></tt> guesses it from the file
-extension [<tt class="docutils literal"><span class="pre">None</span></tt>]
-Can also pass a subclass of <a class="reference internal" href="../topology/base.html#MDAnalysis.topology.base.TopologyReader" title="MDAnalysis.topology.base.TopologyReader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.topology.base.TopologyReader</span></tt></a>
+<dd><p class="first last">provide the file format of the topology file; <code class="docutils literal"><span class="pre">None</span></code> guesses it from the file
+extension [<code class="docutils literal"><span class="pre">None</span></code>]
+Can also pass a subclass of <a class="reference internal" href="../topology/base.html#MDAnalysis.topology.base.TopologyReader" title="MDAnalysis.topology.base.TopologyReader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.topology.base.TopologyReader</span></code></a>
 to define a custom reader to be used on the topology file.</p>
 </dd>
 <dt><em>format</em></dt>
 <dd><p class="first last">provide the file format of the coordinate or trajectory file;
-<tt class="docutils literal"><span class="pre">None</span></tt> guesses it from the file extension. Note that this
+<code class="docutils literal"><span class="pre">None</span></code> guesses it from the file extension. Note that this
 keyword has no effect if a list of file names is supplied because
 the &#8220;chained&#8221; reader has to guess the file format for each
-individual list member. [<tt class="docutils literal"><span class="pre">None</span></tt>]
-Can also pass a subclass of <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Reader</span></tt></a>
+individual list member. [<code class="docutils literal"><span class="pre">None</span></code>]
+Can also pass a subclass of <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Reader</span></code></a>
 to define a custom reader to be used on the trajectory file.</p>
 </dd>
 <dt><em>guess_bonds</em></dt>
@@ -457,16 +467,16 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 which are used in guessing bonds.</p>
 </dd>
 <dt><em>is_anchor</em></dt>
-<dd><p class="first last">When unpickling instances of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a>
+<dd><p class="first last">When unpickling instances of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a>
 existing Universes are searched for one where to anchor those atoms. Set
-to <tt class="docutils literal"><span class="pre">False</span></tt> to prevent this Universe from being considered. [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+to <code class="docutils literal"><span class="pre">False</span></code> to prevent this Universe from being considered. [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 <dt><em>anchor_name</em></dt>
-<dd><p class="first last">Setting to other than <tt class="docutils literal"><span class="pre">None</span></tt> will cause <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a>
+<dd><p class="first last">Setting to other than <code class="docutils literal"><span class="pre">None</span></code> will cause <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a>
 instances pickled from the Universe to only unpickle if a compatible
 Universe with matching <em>anchor_name</em> is found. <em>is_anchor</em> will be ignored in
-this case but will still be honored when unpickling <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a>
-instances pickled with <a href="#id1"><span class="problematic" id="id2">*</span></a>anchor_name*==``None``. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+this case but will still be honored when unpickling <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a>
+instances pickled with <a href="#id1"><span class="problematic" id="id2">*</span></a>anchor_name*==``None``. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -490,45 +500,52 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </li>
 <li><p class="first">If only a topology file without coordinate information is provided
 one will have to load coordinates manually using
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.load_new" title="MDAnalysis.core.AtomGroup.Universe.load_new"><tt class="xref py py-meth docutils literal"><span class="pre">Universe.load_new()</span></tt></a>. The file format of the topology file
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.load_new" title="MDAnalysis.core.AtomGroup.Universe.load_new"><code class="xref py py-meth docutils literal"><span class="pre">Universe.load_new()</span></code></a>. The file format of the topology file
 can be explicitly set with the <em>topology_format</em> keyword.</p>
 </li>
 </ol>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.4: </span>New <em>topology_format</em> and <em>format</em> parameters to override the file
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.4: </span>New <em>topology_format</em> and <em>format</em> parameters to override the file
 format detection.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Added <tt class="docutils literal"><span class="pre">'guess_bonds'</span></tt> keyword to cause topology to be guessed on
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Added <code class="docutils literal"><span class="pre">'guess_bonds'</span></code> keyword to cause topology to be guessed on
 Universe creation.
-Deprecated <tt class="docutils literal"><span class="pre">'bonds'</span></tt> keyword, use <tt class="docutils literal"><span class="pre">'guess_bonds'</span></tt> instead.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Added the <em>is_anchor</em> and <em>anchor_name</em> keywords for finer behavior
-control when unpickling instances of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a>.</p>
+Deprecated <code class="docutils literal"><span class="pre">'bonds'</span></code> keyword, use <code class="docutils literal"><span class="pre">'guess_bonds'</span></code> instead.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Added the <em>is_anchor</em> and <em>anchor_name</em> keywords for finer behavior
+control when unpickling instances of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a>.</p>
+</div>
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Universe.angles">
-<tt class="descname">angles</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.angles"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.angles" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a <tt class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></tt>
+<code class="descname">angles</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.angles" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns a <code class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></code>
 of all angles in the Universe</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.2: </span>Now can return empty TopologyGroup</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.2: </span>Now can return empty TopologyGroup</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Universe.bonds">
-<tt class="descname">bonds</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.bonds" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a <tt class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></tt> of all
+<code class="descname">bonds</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.bonds" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns a <code class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></code> of all
 bonds in the Universe.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Now a lazily built <tt class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></tt></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.2: </span>Now can return empty TopologyGroup</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Now a lazily built <code class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></code></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.2: </span>Now can return empty TopologyGroup</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.Universe.build_topology">
-<tt class="descname">build_topology</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.build_topology"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.build_topology" title="Permalink to this definition">¶</a></dt>
+<code class="descname">build_topology</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.build_topology"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.build_topology" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bond angle and dihedral information is lazily constructed into the
 Universe.</p>
 <p>This method forces all this information to be loaded.</p>
@@ -536,89 +553,93 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Universe.coord">
-<tt class="descname">coord</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.coord"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.coord" title="Permalink to this definition">¶</a></dt>
+<code class="descname">coord</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.coord" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reference to current timestep and coordinates of universe.</p>
-<p>The raw trajectory coordinates are <tt class="xref py py-attr docutils literal"><span class="pre">Universe.coord.positions</span></tt>,
-represented as a <tt class="xref py py-class docutils literal"><span class="pre">numpy.float32</span></tt> array.</p>
-<p>Because <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.coord" title="MDAnalysis.core.AtomGroup.Universe.coord"><tt class="xref py py-attr docutils literal"><span class="pre">coord</span></tt></a> is a reference to a
-<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>, it changes its contents
+<p>The raw trajectory coordinates are <code class="xref py py-attr docutils literal"><span class="pre">Universe.coord.positions</span></code>,
+represented as a <code class="xref py py-class docutils literal"><span class="pre">numpy.float32</span></code> array.</p>
+<p>Because <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.coord" title="MDAnalysis.core.AtomGroup.Universe.coord"><code class="xref py py-attr docutils literal"><span class="pre">coord</span></code></a> is a reference to a
+<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>, it changes its contents
 while one is stepping through the trajectory.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">In order to access the coordinates it is probably better to use the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><tt class="xref py py-meth docutils literal"><span class="pre">AtomGroup.coordinates()</span></tt></a> method; for instance, all coordinates
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><code class="xref py py-meth docutils literal"><span class="pre">AtomGroup.coordinates()</span></code></a> method; for instance, all coordinates
 of the Universe as a numpy array:
-<tt class="xref py py-meth docutils literal"><span class="pre">Universe.atoms.coordinates()</span></tt>.</p>
+<code class="xref py py-meth docutils literal"><span class="pre">Universe.atoms.coordinates()</span></code>.</p>
 </div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Universe.dihedrals">
-<tt class="descname">dihedrals</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.dihedrals"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.dihedrals" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a <tt class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></tt>
+<code class="descname">dihedrals</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.dihedrals" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns a <code class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></code>
 of all dihedrals in the Universe</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.2: </span>Now can return empty TopologyGroup</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.2: </span>Now can return empty TopologyGroup</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Universe.dimensions">
-<tt class="descname">dimensions</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.dimensions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dimensions</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>Current dimensions of the unitcell</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Universe.fragments">
-<tt class="descname">fragments</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.fragments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.fragments" title="Permalink to this definition">¶</a></dt>
+<code class="descname">fragments</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.fragments" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read only tuple of fragments in the Universe</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Universe.impropers">
-<tt class="descname">impropers</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.impropers"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.impropers" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a <tt class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></tt>
+<code class="descname">impropers</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.impropers" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns a <code class="xref py py-class docutils literal"><span class="pre">TopologyGroup</span></code>
 of all improper dihedrals in the Universe</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.2: </span>Now can return empty TopologyGroup</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.2: </span>Now can return empty TopologyGroup</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Universe.is_anchor">
-<tt class="descname">is_anchor</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.is_anchor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.is_anchor" title="Permalink to this definition">¶</a></dt>
+<code class="descname">is_anchor</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.is_anchor" title="Permalink to this definition">¶</a></dt>
 <dd><p>Whether this Universe will be checked for anchoring when unpickling
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> instances</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> instances</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.Universe.load_new">
-<tt class="descname">load_new</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.load_new"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.load_new" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_new</code><span class="sig-paren">(</span><em>filename</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.load_new"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.load_new" title="Permalink to this definition">¶</a></dt>
 <dd><p>Load coordinates from <em>filename</em>, using the suffix to detect file format.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">the coordinate file (single frame or trajectory) <em>or</em> a list of
 filenames, which are read one after another.</p>
 </dd>
 <dt><em>permissive</em></dt>
-<dd><p class="first last">currently only relevant for PDB files: Set to <tt class="docutils literal"><span class="pre">True</span></tt> in order to ignore most errors
-and read typical MD simulation PDB files; set to <tt class="docutils literal"><span class="pre">False</span></tt> to read with the Bio.PDB reader,
-which can be useful for real Protein Databank PDB files. <tt class="docutils literal"><span class="pre">None</span></tt>  selects the
-MDAnalysis default (which is set in <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt>) [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">currently only relevant for PDB files: Set to <code class="docutils literal"><span class="pre">True</span></code> in order to ignore most errors
+and read typical MD simulation PDB files; set to <code class="docutils literal"><span class="pre">False</span></code> to read with the Bio.PDB reader,
+which can be useful for real Protein Databank PDB files. <code class="docutils literal"><span class="pre">None</span></code>  selects the
+MDAnalysis default (which is set in <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code>) [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>format</em></dt>
 <dd><p class="first last">provide the file format of the coordinate or trajectory file;
-<tt class="docutils literal"><span class="pre">None</span></tt> guesses it from the file extension. Note that this
+<code class="docutils literal"><span class="pre">None</span></code> guesses it from the file extension. Note that this
 keyword has no effect if a list of file names is supplied because
 the &#8220;chained&#8221; reader has to guess the file format for each
-individual list member [<tt class="docutils literal"><span class="pre">None</span></tt>]
-Can also pass a subclass of <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Reader</span></tt></a>
+individual list member [<code class="docutils literal"><span class="pre">None</span></code>]
+Can also pass a subclass of <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Reader" title="MDAnalysis.coordinates.base.Reader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.base.Reader</span></code></a>
 to define a custom reader to be used on the trajectory file.</p>
 </dd>
 <dt><em>kwargs</em></dt>
@@ -627,49 +648,50 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">(filename, trajectory_format) or <tt class="docutils literal"><span class="pre">None</span></tt> if <em>filename</em> == <tt class="docutils literal"><span class="pre">None</span></tt></p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">(filename, trajectory_format) or <code class="docutils literal"><span class="pre">None</span></code> if <em>filename</em> == <code class="docutils literal"><span class="pre">None</span></code></p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">TypeError</span></tt> if trajectory format can not be
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">TypeError</span></code> if trajectory format can not be
 determined or no appropriate trajectory reader found</p>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>If a list or sequence that is provided for <em>filename</em>  only contains a single entry
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>If a list or sequence that is provided for <em>filename</em>  only contains a single entry
 then it is treated as single coordinate file. This has the consequence that it is
-not read by the <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.ChainReader" title="MDAnalysis.coordinates.base.ChainReader"><tt class="xref py py-class docutils literal"><span class="pre">ChainReader</span></tt></a> but directly by
+not read by the <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.ChainReader" title="MDAnalysis.coordinates.base.ChainReader"><code class="xref py py-class docutils literal"><span class="pre">ChainReader</span></code></a> but directly by
 its specialized file format reader, which typically has more features than the
-<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.ChainReader" title="MDAnalysis.coordinates.base.ChainReader"><tt class="xref py py-class docutils literal"><span class="pre">ChainReader</span></tt></a>.</p>
+<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.ChainReader" title="MDAnalysis.coordinates.base.ChainReader"><code class="xref py py-class docutils literal"><span class="pre">ChainReader</span></code></a>.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.Universe.make_anchor">
-<tt class="descname">make_anchor</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.make_anchor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.make_anchor" title="Permalink to this definition">¶</a></dt>
+<code class="descname">make_anchor</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.make_anchor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.make_anchor" title="Permalink to this definition">¶</a></dt>
 <dd><p>Add this Universe to the list where anchors are searched for when unpickling
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> instances. Silently proceeds if it
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> instances. Silently proceeds if it
 is already on the list.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.Universe.remove_anchor">
-<tt class="descname">remove_anchor</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.remove_anchor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.remove_anchor" title="Permalink to this definition">¶</a></dt>
+<code class="descname">remove_anchor</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.remove_anchor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.remove_anchor" title="Permalink to this definition">¶</a></dt>
 <dd><p>Remove this Universe from the list where anchors are searched for when unpickling
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> instances. Silently proceeds if it
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> instances. Silently proceeds if it
 is already not on the list.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.Universe.selectAtoms">
-<tt class="descname">selectAtoms</tt><big>(</big><em>*args</em>, <em>**kwds</em><big>)</big><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.selectAtoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">selectAtoms</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.selectAtoms" title="Permalink to this definition">¶</a></dt>
 <dd><p><cite>selectAtoms</cite> is deprecated, use <cite>select_atoms</cite> instead!</p>
 <p>Select atoms using a CHARMM selection string.</p>
 <blockquote>
-<div><p>Returns an <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> with atoms sorted according to their
+<div><p>Returns an <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> with atoms sorted according to their
 index in the psf (this is to ensure that there aren&#8217;t any duplicates,
 which can happen with complicated selections).</p>
-<p>Existing <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> objects can be passed as named arguments,
+<p>Existing <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> objects can be passed as named arguments,
 which will then be available to the selection parser.</p>
 <p>Subselections can be grouped with parentheses.</p>
 <dl class="docutils">
@@ -688,15 +710,15 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">If exact ordering of atoms is required (for instance, for
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.angle" title="MDAnalysis.core.AtomGroup.AtomGroup.angle"><tt class="xref py py-meth docutils literal"><span class="pre">angle()</span></tt></a> or <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.dihedral" title="MDAnalysis.core.AtomGroup.AtomGroup.dihedral"><tt class="xref py py-meth docutils literal"><span class="pre">dihedral()</span></tt></a>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.angle" title="MDAnalysis.core.AtomGroup.AtomGroup.angle"><code class="xref py py-meth docutils literal"><span class="pre">angle()</span></code></a> or <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.dihedral" title="MDAnalysis.core.AtomGroup.AtomGroup.dihedral"><code class="xref py py-meth docutils literal"><span class="pre">dihedral()</span></code></a>
 calculations) then one supplies selections <em>separately</em> in the
-required order. Also, when multiple <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> instances are
-concatenated with the <tt class="docutils literal"><span class="pre">+</span></tt> operator then the order of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>
+required order. Also, when multiple <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> instances are
+concatenated with the <code class="docutils literal"><span class="pre">+</span></code> operator then the order of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>
 instances is preserved and duplicates are not removed.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../selections.html#selection-commands-label"><em>Selection Commands</em></a> for further details and examples.</p>
+<p class="last"><a class="reference internal" href="../selections.html#selection-commands-label"><span>Selection Commands</span></a> for further details and examples.</p>
 </div>
 <p>The selection parser understands the following CASE SENSITIVE <em>keywords</em>:</p>
 <p><strong>Simple selections</strong></p>
@@ -707,20 +729,20 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 is identfied by a hard-coded set of residue names so it  may not
 work for esoteric residues.</dd>
 <dt>segid <em>seg-name</em></dt>
-<dd>select by segid (as given in the topology), e.g. <tt class="docutils literal"><span class="pre">segid</span> <span class="pre">4AKE</span></tt> or <tt class="docutils literal"><span class="pre">segid</span> <span class="pre">DMPC</span></tt></dd>
+<dd>select by segid (as given in the topology), e.g. <code class="docutils literal"><span class="pre">segid</span> <span class="pre">4AKE</span></code> or <code class="docutils literal"><span class="pre">segid</span> <span class="pre">DMPC</span></code></dd>
 <dt>resid <em>residue-number-range</em></dt>
 <dd>resid can take a single residue number or a range of numbers. A range
 consists of two numbers separated by a colon (inclusive) such
-as <tt class="docutils literal"><span class="pre">resid</span> <span class="pre">1:5</span></tt>. A residue number (&#8220;resid&#8221;) is taken directly from the
+as <code class="docutils literal"><span class="pre">resid</span> <span class="pre">1:5</span></code>. A residue number (&#8220;resid&#8221;) is taken directly from the
 topology.</dd>
 <dt>resnum <em>resnum-number-range</em></dt>
 <dd>resnum is the canonical residue number; typically it is set to the residue id
 in the original PDB structure.</dd>
 <dt>resname <em>residue-name</em></dt>
-<dd>select by residue name, e.g. <tt class="docutils literal"><span class="pre">resname</span> <span class="pre">LYS</span></tt></dd>
+<dd>select by residue name, e.g. <code class="docutils literal"><span class="pre">resname</span> <span class="pre">LYS</span></code></dd>
 <dt>name <em>atom-name</em></dt>
 <dd>select by atom name (as given in the topology). Often, this is force
-field dependent. Example: <tt class="docutils literal"><span class="pre">name</span> <span class="pre">CA</span></tt> (for C&amp;alpha; atoms) or <tt class="docutils literal"><span class="pre">name</span> <span class="pre">OW</span></tt> (for SPC water oxygen)</dd>
+field dependent. Example: <code class="docutils literal"><span class="pre">name</span> <span class="pre">CA</span></code> (for C&amp;alpha; atoms) or <code class="docutils literal"><span class="pre">name</span> <span class="pre">OW</span></code> (for SPC water oxygen)</dd>
 <dt>type <em>atom-type</em></dt>
 <dd>select by atom type; this is either a string or a number and depends on
 the force field; it is read from the topology file (e.g. the CHARMM PSF
@@ -728,7 +750,7 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 PDB or GRO file is used as a topology.</dd>
 <dt>atom <em>seg-name</em>  <em>residue-number</em>  <em>atom-name</em></dt>
 <dd>a selector for a single atom consisting of segid resid atomname,
-e.g. <tt class="docutils literal"><span class="pre">DMPC</span> <span class="pre">1</span> <span class="pre">C2</span></tt> selects the C2 carbon of the first residue of the DMPC
+e.g. <code class="docutils literal"><span class="pre">DMPC</span> <span class="pre">1</span> <span class="pre">C2</span></code> selects the C2 carbon of the first residue of the DMPC
 segment</dd>
 <dt>altloc <em>alternative-location</em></dt>
 <dd>a selection for atoms where alternative locations are available,
@@ -741,11 +763,11 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <blockquote>
 <div><dl class="docutils">
 <dt>not</dt>
-<dd>all atoms not in the selection, e.g. <tt class="docutils literal"><span class="pre">not</span> <span class="pre">protein</span></tt> selects
+<dd>all atoms not in the selection, e.g. <code class="docutils literal"><span class="pre">not</span> <span class="pre">protein</span></code> selects
 all atoms that aren&#8217;t part of a protein</dd>
 <dt>and, or</dt>
 <dd>combine two selections according to the rules of boolean algebra,
-e.g. <tt class="docutils literal"><span class="pre">protein</span> <span class="pre">and</span> <span class="pre">not</span> <span class="pre">(resname</span> <span class="pre">ALA</span> <span class="pre">or</span> <span class="pre">resname</span> <span class="pre">LYS)</span></tt> selects all atoms
+e.g. <code class="docutils literal"><span class="pre">protein</span> <span class="pre">and</span> <span class="pre">not</span> <span class="pre">(resname</span> <span class="pre">ALA</span> <span class="pre">or</span> <span class="pre">resname</span> <span class="pre">LYS)</span></code> selects all atoms
 that belong to a protein, but are not in a lysine or alanine residue</dd>
 </dl>
 </div></blockquote>
@@ -754,17 +776,17 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <div><dl class="docutils">
 <dt>around <em>distance</em>  <em>selection</em></dt>
 <dd>selects all atoms a certain cutoff away from another selection,
-e.g. <tt class="docutils literal"><span class="pre">around</span> <span class="pre">3.5</span> <span class="pre">protein</span></tt> selects all atoms not belonging to protein
+e.g. <code class="docutils literal"><span class="pre">around</span> <span class="pre">3.5</span> <span class="pre">protein</span></code> selects all atoms not belonging to protein
 that are within 3.5 Angstroms from the protein</dd>
 <dt>point <em>x</em> <em>y</em> <em>z</em>  <em>distance</em></dt>
 <dd>selects all atoms within a cutoff of a point in space, make sure
-coordinate is separated by spaces, e.g. <tt class="docutils literal"><span class="pre">point</span> <span class="pre">5.0</span> <span class="pre">5.0</span> <span class="pre">5.0</span>&nbsp; <span class="pre">3.5</span></tt> selects
+coordinate is separated by spaces, e.g. <code class="docutils literal"><span class="pre">point</span> <span class="pre">5.0</span> <span class="pre">5.0</span> <span class="pre">5.0</span>&nbsp; <span class="pre">3.5</span></code> selects
 all atoms within 3.5 Angstroms of the coordinate (5.0, 5.0, 5.0)</dd>
 <dt>prop [abs] <em>property</em>  <em>operator</em>  <em>value</em></dt>
 <dd>selects atoms based on position, using <em>property</em>  <strong>x</strong>, <strong>y</strong>, or
 <strong>z</strong> coordinate. Supports the <strong>abs</strong> keyword (for absolute value) and
-the following <em>operators</em>: <strong>&lt;, &gt;, &lt;=, &gt;=, ==, !=</strong>. For example, <tt class="docutils literal"><span class="pre">prop</span> <span class="pre">z</span> <span class="pre">&gt;=</span> <span class="pre">5.0</span></tt>
-selects all atoms with z coordinate greater than 5.0; <tt class="docutils literal"><span class="pre">prop</span> <span class="pre">abs</span> <span class="pre">z</span> <span class="pre">&lt;=</span> <span class="pre">5.0</span></tt>
+the following <em>operators</em>: <strong>&lt;, &gt;, &lt;=, &gt;=, ==, !=</strong>. For example, <code class="docutils literal"><span class="pre">prop</span> <span class="pre">z</span> <span class="pre">&gt;=</span> <span class="pre">5.0</span></code>
+selects all atoms with z coordinate greater than 5.0; <code class="docutils literal"><span class="pre">prop</span> <span class="pre">abs</span> <span class="pre">z</span> <span class="pre">&lt;=</span> <span class="pre">5.0</span></code>
 selects all atoms within -5.0 &lt;= z &lt;= 5.0.</dd>
 </dl>
 </div></blockquote>
@@ -781,9 +803,9 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <div><dl class="docutils">
 <dt>bynum <em>index-range</em></dt>
 <dd>selects all atoms within a range of (1-based) inclusive indices,
-e.g. <tt class="docutils literal"><span class="pre">bynum</span> <span class="pre">1</span></tt> selects the first atom in the universe; <tt class="docutils literal"><span class="pre">bynum</span> <span class="pre">5:10</span></tt>
+e.g. <code class="docutils literal"><span class="pre">bynum</span> <span class="pre">1</span></code> selects the first atom in the universe; <code class="docutils literal"><span class="pre">bynum</span> <span class="pre">5:10</span></code>
 selects atoms 5 through 10 inclusive. All atoms in the
-<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> are consecutively numbered, and the index
+<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> are consecutively numbered, and the index
 runs from 1 up to the total number of atoms.</dd>
 </dl>
 </div></blockquote>
@@ -791,34 +813,36 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <blockquote>
 <div><dl class="docutils">
 <dt>group <em>group-name</em></dt>
-<dd>selects the atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> passed to the function as an
+<dd>selects the atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> passed to the function as an
 argument named <em>group-name</em>. Only the atoms common to <em>group-name</em> and the
-instance <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> was called from will be considered.
+instance <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> was called from will be considered.
 <em>group-name</em> will be included in the parsing just by comparison of atom indices.
 This means that it is up to the user to make sure they were defined in an
-appropriate <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>.</dd>
+appropriate <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>.</dd>
 <dt>fullgroup <em>group-name</em></dt>
-<dd>just like the <tt class="docutils literal"><span class="pre">group</span></tt> keyword with the difference that all the atoms of
+<dd>just like the <code class="docutils literal"><span class="pre">group</span></code> keyword with the difference that all the atoms of
 <em>group-name</em> are included. The resulting selection may therefore have atoms
-that were initially absent from the instance <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> was
+that were initially absent from the instance <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> was
 called from.</dd>
 </dl>
 </div></blockquote>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.4: </span>Added <em>resnum</em> selection.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.1: </span>Added <em>group</em> and <em>fullgroup</em> selections.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.4: </span>Added <em>resnum</em> selection.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.1: </span>Added <em>group</em> and <em>fullgroup</em> selections.</p>
+</div>
 </div></blockquote>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.Universe.select_atoms">
-<tt class="descname">select_atoms</tt><big>(</big><em>sel</em>, <em>*othersel</em>, <em>**selgroups</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.select_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">select_atoms</code><span class="sig-paren">(</span><em>sel</em>, <em>*othersel</em>, <em>**selgroups</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.select_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Select atoms using a CHARMM selection string.</p>
-<p>Returns an <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> with atoms sorted according to their
+<p>Returns an <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> with atoms sorted according to their
 index in the psf (this is to ensure that there aren&#8217;t any duplicates,
 which can happen with complicated selections).</p>
-<p>Existing <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> objects can be passed as named arguments,
+<p>Existing <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> objects can be passed as named arguments,
 which will then be available to the selection parser.</p>
 <p>Subselections can be grouped with parentheses.</p>
 <dl class="docutils">
@@ -837,15 +861,15 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">If exact ordering of atoms is required (for instance, for
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.angle" title="MDAnalysis.core.AtomGroup.AtomGroup.angle"><tt class="xref py py-meth docutils literal"><span class="pre">angle()</span></tt></a> or <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.dihedral" title="MDAnalysis.core.AtomGroup.AtomGroup.dihedral"><tt class="xref py py-meth docutils literal"><span class="pre">dihedral()</span></tt></a>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.angle" title="MDAnalysis.core.AtomGroup.AtomGroup.angle"><code class="xref py py-meth docutils literal"><span class="pre">angle()</span></code></a> or <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.dihedral" title="MDAnalysis.core.AtomGroup.AtomGroup.dihedral"><code class="xref py py-meth docutils literal"><span class="pre">dihedral()</span></code></a>
 calculations) then one supplies selections <em>separately</em> in the
-required order. Also, when multiple <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> instances are
-concatenated with the <tt class="docutils literal"><span class="pre">+</span></tt> operator then the order of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>
+required order. Also, when multiple <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> instances are
+concatenated with the <code class="docutils literal"><span class="pre">+</span></code> operator then the order of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>
 instances is preserved and duplicates are not removed.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../selections.html#selection-commands-label"><em>Selection Commands</em></a> for further details and examples.</p>
+<p class="last"><a class="reference internal" href="../selections.html#selection-commands-label"><span>Selection Commands</span></a> for further details and examples.</p>
 </div>
 <p>The selection parser understands the following CASE SENSITIVE <em>keywords</em>:</p>
 <p><strong>Simple selections</strong></p>
@@ -856,20 +880,20 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 is identfied by a hard-coded set of residue names so it  may not
 work for esoteric residues.</dd>
 <dt>segid <em>seg-name</em></dt>
-<dd>select by segid (as given in the topology), e.g. <tt class="docutils literal"><span class="pre">segid</span> <span class="pre">4AKE</span></tt> or <tt class="docutils literal"><span class="pre">segid</span> <span class="pre">DMPC</span></tt></dd>
+<dd>select by segid (as given in the topology), e.g. <code class="docutils literal"><span class="pre">segid</span> <span class="pre">4AKE</span></code> or <code class="docutils literal"><span class="pre">segid</span> <span class="pre">DMPC</span></code></dd>
 <dt>resid <em>residue-number-range</em></dt>
 <dd>resid can take a single residue number or a range of numbers. A range
 consists of two numbers separated by a colon (inclusive) such
-as <tt class="docutils literal"><span class="pre">resid</span> <span class="pre">1:5</span></tt>. A residue number (&#8220;resid&#8221;) is taken directly from the
+as <code class="docutils literal"><span class="pre">resid</span> <span class="pre">1:5</span></code>. A residue number (&#8220;resid&#8221;) is taken directly from the
 topology.</dd>
 <dt>resnum <em>resnum-number-range</em></dt>
 <dd>resnum is the canonical residue number; typically it is set to the residue id
 in the original PDB structure.</dd>
 <dt>resname <em>residue-name</em></dt>
-<dd>select by residue name, e.g. <tt class="docutils literal"><span class="pre">resname</span> <span class="pre">LYS</span></tt></dd>
+<dd>select by residue name, e.g. <code class="docutils literal"><span class="pre">resname</span> <span class="pre">LYS</span></code></dd>
 <dt>name <em>atom-name</em></dt>
 <dd>select by atom name (as given in the topology). Often, this is force
-field dependent. Example: <tt class="docutils literal"><span class="pre">name</span> <span class="pre">CA</span></tt> (for C&amp;alpha; atoms) or <tt class="docutils literal"><span class="pre">name</span> <span class="pre">OW</span></tt> (for SPC water oxygen)</dd>
+field dependent. Example: <code class="docutils literal"><span class="pre">name</span> <span class="pre">CA</span></code> (for C&amp;alpha; atoms) or <code class="docutils literal"><span class="pre">name</span> <span class="pre">OW</span></code> (for SPC water oxygen)</dd>
 <dt>type <em>atom-type</em></dt>
 <dd>select by atom type; this is either a string or a number and depends on
 the force field; it is read from the topology file (e.g. the CHARMM PSF
@@ -877,7 +901,7 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 PDB or GRO file is used as a topology.</dd>
 <dt>atom <em>seg-name</em>  <em>residue-number</em>  <em>atom-name</em></dt>
 <dd>a selector for a single atom consisting of segid resid atomname,
-e.g. <tt class="docutils literal"><span class="pre">DMPC</span> <span class="pre">1</span> <span class="pre">C2</span></tt> selects the C2 carbon of the first residue of the DMPC
+e.g. <code class="docutils literal"><span class="pre">DMPC</span> <span class="pre">1</span> <span class="pre">C2</span></code> selects the C2 carbon of the first residue of the DMPC
 segment</dd>
 <dt>altloc <em>alternative-location</em></dt>
 <dd>a selection for atoms where alternative locations are available,
@@ -890,11 +914,11 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <blockquote>
 <div><dl class="docutils">
 <dt>not</dt>
-<dd>all atoms not in the selection, e.g. <tt class="docutils literal"><span class="pre">not</span> <span class="pre">protein</span></tt> selects
+<dd>all atoms not in the selection, e.g. <code class="docutils literal"><span class="pre">not</span> <span class="pre">protein</span></code> selects
 all atoms that aren&#8217;t part of a protein</dd>
 <dt>and, or</dt>
 <dd>combine two selections according to the rules of boolean algebra,
-e.g. <tt class="docutils literal"><span class="pre">protein</span> <span class="pre">and</span> <span class="pre">not</span> <span class="pre">(resname</span> <span class="pre">ALA</span> <span class="pre">or</span> <span class="pre">resname</span> <span class="pre">LYS)</span></tt> selects all atoms
+e.g. <code class="docutils literal"><span class="pre">protein</span> <span class="pre">and</span> <span class="pre">not</span> <span class="pre">(resname</span> <span class="pre">ALA</span> <span class="pre">or</span> <span class="pre">resname</span> <span class="pre">LYS)</span></code> selects all atoms
 that belong to a protein, but are not in a lysine or alanine residue</dd>
 </dl>
 </div></blockquote>
@@ -903,17 +927,17 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <div><dl class="docutils">
 <dt>around <em>distance</em>  <em>selection</em></dt>
 <dd>selects all atoms a certain cutoff away from another selection,
-e.g. <tt class="docutils literal"><span class="pre">around</span> <span class="pre">3.5</span> <span class="pre">protein</span></tt> selects all atoms not belonging to protein
+e.g. <code class="docutils literal"><span class="pre">around</span> <span class="pre">3.5</span> <span class="pre">protein</span></code> selects all atoms not belonging to protein
 that are within 3.5 Angstroms from the protein</dd>
 <dt>point <em>x</em> <em>y</em> <em>z</em>  <em>distance</em></dt>
 <dd>selects all atoms within a cutoff of a point in space, make sure
-coordinate is separated by spaces, e.g. <tt class="docutils literal"><span class="pre">point</span> <span class="pre">5.0</span> <span class="pre">5.0</span> <span class="pre">5.0</span>&nbsp; <span class="pre">3.5</span></tt> selects
+coordinate is separated by spaces, e.g. <code class="docutils literal"><span class="pre">point</span> <span class="pre">5.0</span> <span class="pre">5.0</span> <span class="pre">5.0</span>&nbsp; <span class="pre">3.5</span></code> selects
 all atoms within 3.5 Angstroms of the coordinate (5.0, 5.0, 5.0)</dd>
 <dt>prop [abs] <em>property</em>  <em>operator</em>  <em>value</em></dt>
 <dd>selects atoms based on position, using <em>property</em>  <strong>x</strong>, <strong>y</strong>, or
 <strong>z</strong> coordinate. Supports the <strong>abs</strong> keyword (for absolute value) and
-the following <em>operators</em>: <strong>&lt;, &gt;, &lt;=, &gt;=, ==, !=</strong>. For example, <tt class="docutils literal"><span class="pre">prop</span> <span class="pre">z</span> <span class="pre">&gt;=</span> <span class="pre">5.0</span></tt>
-selects all atoms with z coordinate greater than 5.0; <tt class="docutils literal"><span class="pre">prop</span> <span class="pre">abs</span> <span class="pre">z</span> <span class="pre">&lt;=</span> <span class="pre">5.0</span></tt>
+the following <em>operators</em>: <strong>&lt;, &gt;, &lt;=, &gt;=, ==, !=</strong>. For example, <code class="docutils literal"><span class="pre">prop</span> <span class="pre">z</span> <span class="pre">&gt;=</span> <span class="pre">5.0</span></code>
+selects all atoms with z coordinate greater than 5.0; <code class="docutils literal"><span class="pre">prop</span> <span class="pre">abs</span> <span class="pre">z</span> <span class="pre">&lt;=</span> <span class="pre">5.0</span></code>
 selects all atoms within -5.0 &lt;= z &lt;= 5.0.</dd>
 </dl>
 </div></blockquote>
@@ -930,9 +954,9 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <div><dl class="docutils">
 <dt>bynum <em>index-range</em></dt>
 <dd>selects all atoms within a range of (1-based) inclusive indices,
-e.g. <tt class="docutils literal"><span class="pre">bynum</span> <span class="pre">1</span></tt> selects the first atom in the universe; <tt class="docutils literal"><span class="pre">bynum</span> <span class="pre">5:10</span></tt>
+e.g. <code class="docutils literal"><span class="pre">bynum</span> <span class="pre">1</span></code> selects the first atom in the universe; <code class="docutils literal"><span class="pre">bynum</span> <span class="pre">5:10</span></code>
 selects atoms 5 through 10 inclusive. All atoms in the
-<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> are consecutively numbered, and the index
+<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> are consecutively numbered, and the index
 runs from 1 up to the total number of atoms.</dd>
 </dl>
 </div></blockquote>
@@ -940,28 +964,30 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <blockquote>
 <div><dl class="docutils">
 <dt>group <em>group-name</em></dt>
-<dd>selects the atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> passed to the function as an
+<dd>selects the atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> passed to the function as an
 argument named <em>group-name</em>. Only the atoms common to <em>group-name</em> and the
-instance <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> was called from will be considered.
+instance <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> was called from will be considered.
 <em>group-name</em> will be included in the parsing just by comparison of atom indices.
 This means that it is up to the user to make sure they were defined in an
-appropriate <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>.</dd>
+appropriate <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>.</dd>
 <dt>fullgroup <em>group-name</em></dt>
-<dd>just like the <tt class="docutils literal"><span class="pre">group</span></tt> keyword with the difference that all the atoms of
+<dd>just like the <code class="docutils literal"><span class="pre">group</span></code> keyword with the difference that all the atoms of
 <em>group-name</em> are included. The resulting selection may therefore have atoms
-that were initially absent from the instance <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> was
+that were initially absent from the instance <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> was
 called from.</dd>
 </dl>
 </div></blockquote>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.4: </span>Added <em>resnum</em> selection.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8.1: </span>Added <em>group</em> and <em>fullgroup</em> selections.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.4: </span>Added <em>resnum</em> selection.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8.1: </span>Added <em>group</em> and <em>fullgroup</em> selections.</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Universe.trajectory">
-<tt class="descname">trajectory</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Universe.trajectory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.trajectory" title="Permalink to this definition">¶</a></dt>
+<code class="descname">trajectory</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Universe.trajectory" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reference to trajectory reader object containing trajectory data.</p>
 </dd></dl>
 
@@ -969,31 +995,31 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="function">
 <dt id="MDAnalysis.core.AtomGroup.Merge">
-<tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">Merge</tt><big>(</big><em>*args</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Merge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Merge" title="Permalink to this definition">¶</a></dt>
-<dd><p>Return a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> from two or more <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> instances.</p>
-<p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> instances can come from different Universes, or come
-directly from a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> call.</p>
-<p>It can also be used with a single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> if the user wants to,
+<code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">Merge</code><span class="sig-paren">(</span><em>*args</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Merge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Merge" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> from two or more <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> instances.</p>
+<p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> instances can come from different Universes, or come
+directly from a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> call.</p>
+<p>It can also be used with a single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> if the user wants to,
 for example, re-order the atoms in the Universe.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body">One or more <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> instances.</td>
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body">One or more <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> instances.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body">an instance of <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">an instance of <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> for too few arguments or if an AtomGroup is
-empty and <tt class="xref py py-exc docutils literal"><span class="pre">TypeError</span></tt> if arguments are not
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> instances.</td>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> for too few arguments or if an AtomGroup is
+empty and <code class="xref py py-exc docutils literal"><span class="pre">TypeError</span></code> if arguments are not
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> instances.</td>
 </tr>
 </tbody>
 </table>
 <p class="rubric">Example</p>
 <p>In this example, protein, ligand, and solvent were externally prepared in
-three different PDB files. They are loaded into separate <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>
+three different PDB files. They are loaded into separate <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>
 objects (where they could be further manipulated, e.g. renumbered,
-relabeled, rotated, ...) The <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Merge" title="MDAnalysis.core.AtomGroup.Merge"><tt class="xref py py-func docutils literal"><span class="pre">Merge()</span></tt></a> command is used to combine all
+relabeled, rotated, ...) The <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Merge" title="MDAnalysis.core.AtomGroup.Merge"><code class="xref py py-func docutils literal"><span class="pre">Merge()</span></code></a> command is used to combine all
 of them together:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">u1</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="s">&quot;protein.pdb&quot;</span><span class="p">)</span>
 <span class="n">u2</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="s">&quot;ligand.pdb&quot;</span><span class="p">)</span>
@@ -1012,31 +1038,31 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="class">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">AtomGroup</tt><big>(</big><em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">AtomGroup</code><span class="sig-paren">(</span><em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="Permalink to this definition">¶</a></dt>
 <dd><p>A group of atoms.</p>
 <blockquote>
 <div>ag = universe.select_atoms(atom-list)</div></blockquote>
 <p>The AtomGroup contains a list of atoms; typically, a AtomGroup is generated
 from a selection. It is build from any list-like collection of
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances. It is also possible to create an empty AtomGroup
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances. It is also possible to create an empty AtomGroup
 from an empty list.</p>
 <p>An AtomGroup can be indexed and sliced like a list:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">ag</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">ag</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
 </pre></div>
 </div>
-<p>will return the first and the last <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> in the group
+<p>will return the first and the last <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> in the group
 whereas the slice</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">ag</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">6</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
 </pre></div>
 </div>
 <p>returns every second element, corresponding to indices 0, 2, and 4.</p>
 <p>It also supports &#8220;advanced slicing&#8221; when the argument is a
-<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or a <a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>:</p>
+<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> or a <a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">aslice</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span>
 <span class="n">ag</span><span class="p">[</span><span class="n">aslice</span><span class="p">]</span>
 </pre></div>
 </div>
-<p>will return a new <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> containing (ag[0], ag[3], ag[-1],
+<p>will return a new <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> containing (ag[0], ag[3], ag[-1],
 ag[10], ag[3]).</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
@@ -1051,70 +1077,77 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <div class="highlight-python"><div class="highlight"><pre><span class="n">ag</span><span class="o">.</span><span class="n">CA</span>
 </pre></div>
 </div>
-<p>will provide a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> of all CA atoms in the
+<p>will provide a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> of all CA atoms in the
 group. These <em>instant selector</em> attributes are auto-generated for
 each atom name encountered in the group.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The name-attribute instant selector access to atoms is mainly
 meant for quick interactive work. Thus it either returns a
-single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> if there is only one matching atom, <em>or</em> a
-new <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> for multiple matches.  This makes it
+single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> if there is only one matching atom, <em>or</em> a
+new <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> for multiple matches.  This makes it
 difficult to use the feature consistently in scripts but it is
 much better for interactive work.</p>
 </div>
-<p>AtomGroup instances are bound to a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>, but only through the
-weak reference <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> has. The connection is lost as soon as the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> goes out of scope.</p>
+<p>AtomGroup instances are bound to a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>, but only through the
+weak reference <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> has. The connection is lost as soon as the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> goes out of scope.</p>
 <p>AtomGroups can also be pickled and unpickled. When pickling, the Atom
 indices are serialized alongside the Universe number-of-atoms, and topology
 and trajectory filenames. When unpickling, all built Universes will be
 searched for one with matching number-of-atoms and filenames. Finer control
-over which <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> gets chosen to base the unpickling on can
+over which <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> gets chosen to base the unpickling on can
 be exerted using the <em>is_anchor</em> and <em>anchor_name</em> flags upon Universe creation
-or the methods/attributes <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.make_anchor" title="MDAnalysis.core.AtomGroup.Universe.make_anchor"><tt class="xref py py-meth docutils literal"><span class="pre">Universe.make_anchor()</span></tt></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.remove_anchor" title="MDAnalysis.core.AtomGroup.Universe.remove_anchor"><tt class="xref py py-meth docutils literal"><span class="pre">Universe.remove_anchor()</span></tt></a>,
-and <tt class="xref py py-attr docutils literal"><span class="pre">Universe.anchor_name</span></tt>.</p>
+or the methods/attributes <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.make_anchor" title="MDAnalysis.core.AtomGroup.Universe.make_anchor"><code class="xref py py-meth docutils literal"><span class="pre">Universe.make_anchor()</span></code></a>, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.remove_anchor" title="MDAnalysis.core.AtomGroup.Universe.remove_anchor"><code class="xref py py-meth docutils literal"><span class="pre">Universe.remove_anchor()</span></code></a>,
+and <code class="xref py py-attr docutils literal"><span class="pre">Universe.anchor_name</span></code>.</p>
 <p class="rubric">References for analysis methods</p>
 <table class="docutils citation" frame="void" id="dima2004" rules="none">
 <colgroup><col class="label" /><col /></colgroup>
 <tbody valign="top">
-<tr><td class="label">[Dima2004]</td><td><em>(<a class="fn-backref" href="#id3">1</a>, <a class="fn-backref" href="#id4">2</a>)</em> Dima, R. I., &amp; Thirumalai, D. (2004). Asymmetry in the
+<tr><td class="label">[Dima2004]</td><td><em>(<a class="fn-backref" href="#id3">1</a>, <a class="fn-backref" href="#id4">2</a>, <a class="fn-backref" href="#id5">3</a>)</em> Dima, R. I., &amp; Thirumalai, D. (2004). Asymmetry in the
 shapes of folded and denatured states of proteins. <em>J
 Phys Chem B</em>, 108(21),
 6564-6570. doi:<a class="reference external" href="http://dx.doi.org/10.1021/jp037128y">10.1021/jp037128y</a></td></tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>An empty AtomGroup can be created and no longer raises a
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.NoDataError" title="MDAnalysis.core.AtomGroup.NoDataError"><code class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></code></a>.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>An empty AtomGroup can be created and no longer raises a
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.NoDataError" title="MDAnalysis.core.AtomGroup.NoDataError"><tt class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></tt></a>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>The size at which cache is used for atom lookup is now stored as variable
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>The size at which cache is used for atom lookup is now stored as variable
 _atomcache_size within the class.
 Added fragments manged property. Is a lazily built, cached entry, similar to residues.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>AtomGroups can now be pickled and unpickled provided compatible Universes
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>AtomGroups can now be pickled and unpickled provided compatible Universes
 are available.
-The follow methods were changed to properties: <tt class="docutils literal"><span class="pre">indices</span></tt>, <tt class="docutils literal"><span class="pre">masses</span></tt>, <tt class="docutils literal"><span class="pre">charges</span></tt>, <tt class="docutils literal"><span class="pre">names</span></tt>,
-<tt class="docutils literal"><span class="pre">types</span></tt>, <tt class="docutils literal"><span class="pre">radii</span></tt>, <tt class="docutils literal"><span class="pre">resids</span></tt>, <tt class="docutils literal"><span class="pre">resnames</span></tt>, <tt class="docutils literal"><span class="pre">resnums</span></tt>, <tt class="docutils literal"><span class="pre">segids</span></tt>.
-Added <tt class="docutils literal"><span class="pre">altLocs</span></tt> and <tt class="docutils literal"><span class="pre">serials</span></tt> properties and setters.
-<tt class="docutils literal"><span class="pre">Torsions</span></tt> and <tt class="docutils literal"><span class="pre">torsion</span></tt> renamed to <tt class="docutils literal"><span class="pre">dihedral</span></tt>.
-The <tt class="docutils literal"><span class="pre">bond</span></tt>, <tt class="docutils literal"><span class="pre">angle</span></tt>, <tt class="docutils literal"><span class="pre">dihedral</span></tt> and <tt class="docutils literal"><span class="pre">improper</span></tt> methods were removed and replaced
+The follow methods were changed to properties: <code class="docutils literal"><span class="pre">indices</span></code>, <code class="docutils literal"><span class="pre">masses</span></code>, <code class="docutils literal"><span class="pre">charges</span></code>, <code class="docutils literal"><span class="pre">names</span></code>,
+<code class="docutils literal"><span class="pre">types</span></code>, <code class="docutils literal"><span class="pre">radii</span></code>, <code class="docutils literal"><span class="pre">resids</span></code>, <code class="docutils literal"><span class="pre">resnames</span></code>, <code class="docutils literal"><span class="pre">resnums</span></code>, <code class="docutils literal"><span class="pre">segids</span></code>.
+Added <code class="docutils literal"><span class="pre">altLocs</span></code> and <code class="docutils literal"><span class="pre">serials</span></code> properties and setters.
+<code class="docutils literal"><span class="pre">Torsions</span></code> and <code class="docutils literal"><span class="pre">torsion</span></code> renamed to <code class="docutils literal"><span class="pre">dihedral</span></code>.
+The <code class="docutils literal"><span class="pre">bond</span></code>, <code class="docutils literal"><span class="pre">angle</span></code>, <code class="docutils literal"><span class="pre">dihedral</span></code> and <code class="docutils literal"><span class="pre">improper</span></code> methods were removed and replaced
 with properties of the same name which return the corresponding object.
-Deprecated <tt class="docutils literal"><span class="pre">selectAtoms</span></tt> in favour of <tt class="docutils literal"><span class="pre">select_atoms</span></tt>.</p>
+Deprecated <code class="docutils literal"><span class="pre">selectAtoms</span></code> in favour of <code class="docutils literal"><span class="pre">select_atoms</span></code>.
+Setters are now plural to match property names.
+Properties referring to residue (<code class="docutils literal"><span class="pre">resids</span></code>, <code class="docutils literal"><span class="pre">resnames</span></code>, <code class="docutils literal"><span class="pre">resnums</span></code>)
+or segment [<code class="docutils literal"><span class="pre">segids</span></code>] properties now yield arrays of length equal to
+<code class="docutils literal"><span class="pre">n_atoms</span></code></p>
+</div>
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup._atoms">
-<tt class="descname">_atoms</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup._atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup._atoms" title="Permalink to this definition">¶</a></dt>
-<dd><p>immutable list of references to the atoms <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> in the
+<code class="descname">_atoms</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup._atoms" title="Permalink to this definition">¶</a></dt>
+<dd><p>immutable list of references to the atoms <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> in the
 group</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup._rebuild_caches">
-<tt class="descname">_rebuild_caches</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup._rebuild_caches"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup._rebuild_caches" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_rebuild_caches</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup._rebuild_caches"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup._rebuild_caches" title="Permalink to this definition">¶</a></dt>
 <dd><p>Rebuild all AtomGroup caches.</p>
 <p>A number of lists and attributes are cached. These caches are lazily
 built the first time they are needed. When editing the topology it
@@ -1125,62 +1158,99 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <ul class="simple">
 <li>atoms (for &#8220;in&#8221; lookup); cache is only built for large systems with
 &gt; 10,000 atoms</li>
-<li>indices (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.indices" title="MDAnalysis.core.AtomGroup.AtomGroup.indices"><tt class="xref py py-meth docutils literal"><span class="pre">AtomGroup.indices()</span></tt></a>)</li>
-<li>masses (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.masses" title="MDAnalysis.core.AtomGroup.AtomGroup.masses"><tt class="xref py py-meth docutils literal"><span class="pre">AtomGroup.masses()</span></tt></a>)</li>
-<li>residues (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="MDAnalysis.core.AtomGroup.AtomGroup.residues"><tt class="xref py py-attr docutils literal"><span class="pre">AtomGroup.residues</span></tt></a>)</li>
-<li>segments (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.segments" title="MDAnalysis.core.AtomGroup.AtomGroup.segments"><tt class="xref py py-attr docutils literal"><span class="pre">AtomGroup.segments</span></tt></a>)</li>
-<li>bonds (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.bonds" title="MDAnalysis.core.AtomGroup.AtomGroup.bonds"><tt class="xref py py-attr docutils literal"><span class="pre">AtomGroup.bonds</span></tt></a>)</li>
-<li>angles (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.angles" title="MDAnalysis.core.AtomGroup.AtomGroup.angles"><tt class="xref py py-attr docutils literal"><span class="pre">AtomGroup.angles</span></tt></a>)</li>
-<li>dihedrals (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.dihedrals" title="MDAnalysis.core.AtomGroup.AtomGroup.dihedrals"><tt class="xref py py-attr docutils literal"><span class="pre">AtomGroup.dihedrals</span></tt></a>)</li>
-<li>improper dihedrals (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.impropers" title="MDAnalysis.core.AtomGroup.AtomGroup.impropers"><tt class="xref py py-attr docutils literal"><span class="pre">AtomGroup.impropers</span></tt></a>)</li>
+<li>indices (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.indices" title="MDAnalysis.core.AtomGroup.AtomGroup.indices"><code class="xref py py-meth docutils literal"><span class="pre">AtomGroup.indices()</span></code></a>)</li>
+<li>masses (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.masses" title="MDAnalysis.core.AtomGroup.AtomGroup.masses"><code class="xref py py-meth docutils literal"><span class="pre">AtomGroup.masses()</span></code></a>)</li>
+<li>residues (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="MDAnalysis.core.AtomGroup.AtomGroup.residues"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.residues</span></code></a>)</li>
+<li>segments (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.segments" title="MDAnalysis.core.AtomGroup.AtomGroup.segments"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.segments</span></code></a>)</li>
+<li>bonds (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.bonds" title="MDAnalysis.core.AtomGroup.AtomGroup.bonds"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.bonds</span></code></a>)</li>
+<li>angles (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.angles" title="MDAnalysis.core.AtomGroup.AtomGroup.angles"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.angles</span></code></a>)</li>
+<li>dihedrals (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.dihedrals" title="MDAnalysis.core.AtomGroup.AtomGroup.dihedrals"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.dihedrals</span></code></a>)</li>
+<li>improper dihedrals (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.impropers" title="MDAnalysis.core.AtomGroup.AtomGroup.impropers"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.impropers</span></code></a>)</li>
 </ul>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup._clear_caches" title="MDAnalysis.core.AtomGroup.AtomGroup._clear_caches"><tt class="xref py py-meth docutils literal"><span class="pre">_clear_caches()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup._clear_caches" title="MDAnalysis.core.AtomGroup.AtomGroup._clear_caches"><code class="xref py py-meth docutils literal"><span class="pre">_clear_caches()</span></code></a></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Added bonds/angles/torsions/impropers to rebuild.
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Added bonds/angles/torsions/impropers to rebuild.
 Reworked how things are rebuilt to avoid code duplication.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup._clear_caches">
-<tt class="descname">_clear_caches</tt><big>(</big><em>*args</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup._clear_caches"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup._clear_caches" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_clear_caches</code><span class="sig-paren">(</span><em>*args</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup._clear_caches"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup._clear_caches" title="Permalink to this definition">¶</a></dt>
 <dd><p>Clear cache for all <em>args</em>.</p>
 <p>If no args are provided, all caches are cleared.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup._rebuild_caches" title="MDAnalysis.core.AtomGroup.AtomGroup._rebuild_caches"><tt class="xref py py-meth docutils literal"><span class="pre">_rebuild_caches()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup._rebuild_caches" title="MDAnalysis.core.AtomGroup.AtomGroup._rebuild_caches"><code class="xref py py-meth docutils literal"><span class="pre">_rebuild_caches()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup._fill_cache">
-<tt class="descname">_fill_cache</tt><big>(</big><em>name</em>, <em>value</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup._fill_cache"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup._fill_cache" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_fill_cache</code><span class="sig-paren">(</span><em>name</em>, <em>value</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup._fill_cache"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup._fill_cache" title="Permalink to this definition">¶</a></dt>
 <dd><p>Populate _cache[name] with value.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.align_principalAxis">
-<tt class="descname">align_principalAxis</tt><big>(</big><em>axis</em>, <em>vector</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.align_principalAxis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.align_principalAxis" title="Permalink to this definition">¶</a></dt>
+<code class="descname">align_principalAxis</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.align_principalAxis" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>align_principalAxis</cite> is deprecated, use <cite>align_principal_axis</cite> instead!</p>
+<p>Align principal axis with index <em>axis</em> with <em>vector</em>.</p>
+<blockquote>
+<div><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>axis</em></dt>
+<dd><p class="first last">Index of the principal axis (0, 1, or 2), as produced by
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.principal_axes" title="MDAnalysis.core.AtomGroup.AtomGroup.principal_axes"><code class="xref py py-meth docutils literal"><span class="pre">principal_axes()</span></code></a>.</p>
+</dd>
+<dt><em>vector</em></dt>
+<dd><p class="first last">A 3D vector such as the z-axis (<code class="docutils literal"><span class="pre">[0,0,1]</span></code>); can be
+anything that looks like a list with three entries.</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
+<p>To align the long axis of a channel (the first principal axis,
+i.e. <em>axis</em> = 0) with the z-axis:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">align_principal_axis</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">])</span>
+<span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&quot;aligned.pdb&quot;</span><span class="p">)</span>
+</pre></div>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.align_principal_axis">
+<code class="descname">align_principal_axis</code><span class="sig-paren">(</span><em>axis</em>, <em>vector</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.align_principal_axis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.align_principal_axis" title="Permalink to this definition">¶</a></dt>
 <dd><p>Align principal axis with index <em>axis</em> with <em>vector</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>axis</em></dt>
 <dd><p class="first last">Index of the principal axis (0, 1, or 2), as produced by
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.principalAxes" title="MDAnalysis.core.AtomGroup.AtomGroup.principalAxes"><tt class="xref py py-meth docutils literal"><span class="pre">principalAxes()</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.principal_axes" title="MDAnalysis.core.AtomGroup.AtomGroup.principal_axes"><code class="xref py py-meth docutils literal"><span class="pre">principal_axes()</span></code></a>.</p>
 </dd>
 <dt><em>vector</em></dt>
-<dd><p class="first last">A 3D vector such as the z-axis (<tt class="docutils literal"><span class="pre">[0,0,1]</span></tt>); can be
+<dd><p class="first last">A 3D vector such as the z-axis (<code class="docutils literal"><span class="pre">[0,0,1]</span></code>); can be
 anything that looks like a list with three entries.</p>
 </dd>
 </dl>
@@ -1190,7 +1260,7 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <p>To align the long axis of a channel (the first principal axis,
 i.e. <em>axis</em> = 0) with the z-axis:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">align_principalAxis</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">])</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">align_principal_axis</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">])</span>
 <span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&quot;aligned.pdb&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
@@ -1198,55 +1268,59 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.altLocs">
-<tt class="descname">altLocs</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.altLocs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.altLocs" title="Permalink to this definition">¶</a></dt>
+<code class="descname">altLocs</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.altLocs" title="Permalink to this definition">¶</a></dt>
 <dd><p>numpy array of the altLocs for all atoms in this group</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.angle">
-<tt class="descname">angle</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.angle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.angle" title="Permalink to this definition">¶</a></dt>
+<code class="descname">angle</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.angle" title="Permalink to this definition">¶</a></dt>
 <dd><p>This AtomGroup represented as an Angle object</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.Angle</span></tt> object</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.Angle</span></code> object</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><cite>ValueError</cite> if the AtomGroup is not length 3</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><cite>ValueError</cite> if the AtomGroup is not length 3</td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.angles">
-<tt class="descname">angles</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.angles"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.angles" title="Permalink to this definition">¶</a></dt>
+<code class="descname">angles</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.angles" title="Permalink to this definition">¶</a></dt>
 <dd><p>All the angles in this AtomGroup</p>
 <p>Note that these angles might extend out of the AtomGroup, to select
 only angles which are entirely contained by the AtomGroup use
 u.angles.atomgroup_intersection(ag, strict=True)</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Now always returns a (possibly empty) TopologyGroup</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Now always returns a (possibly empty) TopologyGroup</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.asphericity">
-<tt class="descname">asphericity</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.asphericity"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.asphericity" title="Permalink to this definition">¶</a></dt>
+<code class="descname">asphericity</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.asphericity"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.asphericity" title="Permalink to this definition">¶</a></dt>
 <dd><p>Asphericity.</p>
-<p>See <a class="reference internal" href="#dima2004">[Dima2004]</a> for background information.</p>
+<p>See <a class="reference internal" href="#dima2004" id="id3">[Dima2004]</a> for background information.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>pbc</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: Move all atoms within primary unit cell before calculation [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -1255,29 +1329,31 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> flag <em>use_pbc</em> when set to <tt class="docutils literal"><span class="pre">True</span></tt> allows the <em>pbc</em>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
 flag to be used by default.</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.atoms">
-<tt class="descname">atoms</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.atoms" title="Permalink to this definition">¶</a></dt>
-<dd><p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> of all atoms in this group.</p>
-<p>If this is a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> then it returns itself. Otherwise, it
-will return a new <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> based on all <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>
+<code class="descname">atoms</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.atoms" title="Permalink to this definition">¶</a></dt>
+<dd><p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> of all atoms in this group.</p>
+<p>If this is a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then it returns itself. Otherwise, it
+will return a new <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> based on all <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>
 instances contained.</p>
-<p>Apply <cite>:func:`list</cite> to <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.atoms"><tt class="xref py py-attr docutils literal"><span class="pre">atoms</span></tt></a> or use <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup._atoms" title="MDAnalysis.core.AtomGroup.AtomGroup._atoms"><tt class="xref py py-attr docutils literal"><span class="pre">_atoms</span></tt></a> if you
-really only need a list of individual <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances.</p>
+<p>Apply <cite>:func:`list</cite> to <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.atoms"><code class="xref py py-attr docutils literal"><span class="pre">atoms</span></code></a> or use <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup._atoms" title="MDAnalysis.core.AtomGroup.AtomGroup._atoms"><code class="xref py py-attr docutils literal"><span class="pre">_atoms</span></code></a> if you
+really only need a list of individual <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.bbox">
-<tt class="descname">bbox</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.bbox"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.bbox" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bbox</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.bbox"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.bbox" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return the bounding box of the selection.</p>
 <p>The lengths A,B,C of the orthorhombic enclosing box are</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">L</span> <span class="o">=</span> <span class="n">AtomGroup</span><span class="o">.</span><span class="n">bbox</span><span class="p">()</span>
@@ -1288,9 +1364,9 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>pbc</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: Move all atoms within the primary unit cell before calculation [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -1299,72 +1375,77 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> flag <em>use_pbc</em> when set to <tt class="docutils literal"><span class="pre">True</span></tt> allows the <em>pbc</em>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
 flag to be used by default.</p>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">[[xmin, ymin, zmin], [xmax, ymax, zmax]]</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">[[xmin, ymin, zmin], [xmax, ymax, zmax]]</td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.2.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.2.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.bfactors">
-<tt class="descname">bfactors</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.bfactors"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.bfactors" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bfactors</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.bfactors" title="Permalink to this definition">¶</a></dt>
 <dd><p>Crystallographic B-factors (from PDB) in A**2.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.bond">
-<tt class="descname">bond</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.bond"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.bond" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bond</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.bond" title="Permalink to this definition">¶</a></dt>
 <dd><p>This AtomGroup represented as a Bond object</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.Bond</span></tt> object</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.Bond</span></code> object</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><cite>ValueError</cite> if the AtomGroup is not length 2</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><cite>ValueError</cite> if the AtomGroup is not length 2</td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.bonds">
-<tt class="descname">bonds</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.bonds" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bonds</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.bonds" title="Permalink to this definition">¶</a></dt>
 <dd><p>All the bonds in this AtomGroup</p>
 <p>Note that these bonds might extend out of the AtomGroup, to select
 only bonds which are entirely contained by the AtomGroup use
 u.bonds.atomgroup_intersection(ag, strict=True)</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Now always returns a (possibly empty) TopologyGroup</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Now always returns a (possibly empty) TopologyGroup</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.bsphere">
-<tt class="descname">bsphere</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.bsphere"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.bsphere" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bsphere</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.bsphere"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.bsphere" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return the bounding sphere of the selection.</p>
 <p>The sphere is calculated relative to the centre of geometry.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>pbc</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: Move all atoms within primary unit cell before calculation [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -1373,34 +1454,96 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> flag <em>use_pbc</em> when set to <tt class="docutils literal"><span class="pre">True</span></tt> allows the <em>pbc</em>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
 flag to be used by default.</p>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><cite>(R, [xcen,ycen,zcen])</cite></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><cite>(R, [xcen,ycen,zcen])</cite></td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.3.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.3.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry">
-<tt class="descname">centerOfGeometry</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.centerOfGeometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry" title="Permalink to this definition">¶</a></dt>
+<code class="descname">centerOfGeometry</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>centerOfGeometry</cite> is deprecated, use <cite>center_of_geometry</cite> instead!</p>
+<p>Center of geometry (also known as centroid) of the selection.</p>
+<blockquote>
+<div><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>pbc</em></dt>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
+flag to be used by default.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass">
+<code class="descname">centerOfMass</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>centerOfMass</cite> is deprecated, use <cite>center_of_mass</cite> instead!</p>
+<p>Center of mass of the selection.</p>
+<blockquote>
+<div><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>pbc</em></dt>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
+flag to be used by default.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry">
+<code class="descname">center_of_geometry</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.center_of_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry" title="Permalink to this definition">¶</a></dt>
 <dd><p>Center of geometry (also known as centroid) of the selection.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>pbc</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: Move all atoms within the primary unit cell before calculation [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -1409,24 +1552,25 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> flag <em>use_pbc</em> when set to <tt class="docutils literal"><span class="pre">True</span></tt> allows the <em>pbc</em>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
 flag to be used by default.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
 </dd></dl>
 
 <dl class="method">
-<dt id="MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass">
-<tt class="descname">centerOfMass</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.centerOfMass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass" title="Permalink to this definition">¶</a></dt>
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.center_of_mass">
+<code class="descname">center_of_mass</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.center_of_mass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.center_of_mass" title="Permalink to this definition">¶</a></dt>
 <dd><p>Center of mass of the selection.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>pbc</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: Move all atoms within the primary unit cell before calculation [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -1435,24 +1579,25 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> flag <em>use_pbc</em> when set to <tt class="docutils literal"><span class="pre">True</span></tt> allows the <em>pbc</em>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
 flag to be used by default.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.centroid">
-<tt class="descname">centroid</tt><big>(</big><em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.centroid" title="Permalink to this definition">¶</a></dt>
+<code class="descname">centroid</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.centroid" title="Permalink to this definition">¶</a></dt>
 <dd><p>Center of geometry (also known as centroid) of the selection.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>pbc</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: Move all atoms within the primary unit cell before calculation [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -1461,87 +1606,94 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> flag <em>use_pbc</em> when set to <tt class="docutils literal"><span class="pre">True</span></tt> allows the <em>pbc</em>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
 flag to be used by default.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.charges">
-<tt class="descname">charges</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.charges"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.charges" title="Permalink to this definition">¶</a></dt>
+<code class="descname">charges</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.charges" title="Permalink to this definition">¶</a></dt>
 <dd><p>Array of partial charges of the atoms (as defined in the topology)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.coordinates">
-<tt class="descname">coordinates</tt><big>(</big><em>ts=None</em>, <em>copy=False</em>, <em>dtype=&lt;type 'numpy.float32'&gt;</em><big>)</big><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="Permalink to this definition">¶</a></dt>
+<code class="descname">coordinates</code><span class="sig-paren">(</span><em>ts=None</em>, <em>copy=False</em>, <em>dtype=&lt;type 'numpy.float32'&gt;</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="Permalink to this definition">¶</a></dt>
 <dd><p>NumPy array of the coordinates.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="MDAnalysis.core.AtomGroup.AtomGroup.positions"><tt class="xref py py-attr docutils literal"><span class="pre">positions</span></tt></a> and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.get_positions"><tt class="xref py py-meth docutils literal"><span class="pre">get_positions()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="MDAnalysis.core.AtomGroup.AtomGroup.positions"><code class="xref py py-attr docutils literal"><span class="pre">positions</span></code></a> and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.get_positions"><code class="xref py py-meth docutils literal"><span class="pre">get_positions()</span></code></a></p>
+</div>
+<div class="deprecated">
+<p><span class="versionmodified">Deprecated since version 0.7.6: </span>In new scripts use <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.get_positions"><code class="xref py py-meth docutils literal"><span class="pre">AtomGroup.get_positions()</span></code></a> preferrably.</p>
 </div>
-<p class="deprecated">
-<span class="versionmodified">Deprecated since version 0.7.6: </span>In new scripts use <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.get_positions"><tt class="xref py py-meth docutils literal"><span class="pre">AtomGroup.get_positions()</span></tt></a> preferrably.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.dihedral">
-<tt class="descname">dihedral</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.dihedral"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.dihedral" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dihedral</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.dihedral" title="Permalink to this definition">¶</a></dt>
 <dd><p>This AtomGroup represented as a Dihedral object</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.Dihedral</span></tt> object</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.Dihedral</span></code> object</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><cite>ValueError</cite> if the AtomGroup is not length 4</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><cite>ValueError</cite> if the AtomGroup is not length 4</td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.dihedrals">
-<tt class="descname">dihedrals</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.dihedrals"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.dihedrals" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dihedrals</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.dihedrals" title="Permalink to this definition">¶</a></dt>
 <dd><p>All the dihedrals in this AtomGroup</p>
 <p>Note that these dihedrals might extend out of the AtomGroup, to select
 only dihedrals which are entirely contained by the AtomGroup use
 u.dihedrals.atomgroup_intersection(ag, strict=True)</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Now always returns a (possibly empty) TopologyGroup</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Now always returns a (possibly empty) TopologyGroup</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.dimensions">
-<tt class="descname">dimensions</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.dimensions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.dimensions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dimensions</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.dimensions" title="Permalink to this definition">¶</a></dt>
 <dd><p>Dimensions of the Universe to which the group belongs, at the current time step.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.forces">
-<tt class="descname">forces</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.forces" title="Permalink to this definition">¶</a></dt>
+<code class="descname">forces</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.forces" title="Permalink to this definition">¶</a></dt>
 <dd><p>Forces on the atoms in the AtomGroup.</p>
 <p>The forces can be changed by assigning an array of the appropriate
 shape, i.e. either Nx3 to assign individual force or 3, to assign
-the <em>same</em> force to all atoms (e.g. <tt class="docutils literal"><span class="pre">ag.forces</span> <span class="pre">=</span> <span class="pre">array([0,0,0])</span></tt>
+the <em>same</em> force to all atoms (e.g. <code class="docutils literal"><span class="pre">ag.forces</span> <span class="pre">=</span> <span class="pre">array([0,0,0])</span></code>
 will set all forces to (0.,0.,0.)).</p>
-<p>For more control use the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_forces" title="MDAnalysis.core.AtomGroup.AtomGroup.get_forces"><tt class="xref py py-meth docutils literal"><span class="pre">get_forces()</span></tt></a> and
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_forces" title="MDAnalysis.core.AtomGroup.AtomGroup.set_forces"><tt class="xref py py-meth docutils literal"><span class="pre">set_forces()</span></tt></a> methods.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<p>For more control use the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_forces" title="MDAnalysis.core.AtomGroup.AtomGroup.get_forces"><code class="xref py py-meth docutils literal"><span class="pre">get_forces()</span></code></a> and
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_forces" title="MDAnalysis.core.AtomGroup.AtomGroup.set_forces"><code class="xref py py-meth docutils literal"><span class="pre">set_forces()</span></code></a> methods.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.fragments">
-<tt class="descname">fragments</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.fragments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.fragments" title="Permalink to this definition">¶</a></dt>
+<code class="descname">fragments</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.fragments" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read-only list of fragments.</p>
 <p>Contains all fragments that any Atom in this AtomGroup is part of, the contents of
 the fragments may extend beyond the contents of this AtomGroup.</p>
@@ -1549,32 +1701,32 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.get_forces">
-<tt class="descname">get_forces</tt><big>(</big><em>ts=None</em>, <em>copy=False</em>, <em>dtype=&lt;type 'numpy.float32'&gt;</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.get_forces"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_forces" title="Permalink to this definition">¶</a></dt>
+<code class="descname">get_forces</code><span class="sig-paren">(</span><em>ts=None</em>, <em>copy=False</em>, <em>dtype=&lt;type 'numpy.float32'&gt;</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.get_forces"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_forces" title="Permalink to this definition">¶</a></dt>
 <dd><p>Get a NumPy array of the atomic forces (if available).
 Currently only supported for Gromacs .trr trajectories.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>ts</em></dt>
 <dd><p class="first last">If <em>ts</em> is provided then positions are read from that
-<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instead of
+<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instead of
 the one from the current trajectory belonging to this universe.
 The <em>ts</em> is indexed with the indices returned by
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.indices" title="MDAnalysis.core.AtomGroup.AtomGroup.indices"><tt class="xref py py-meth docutils literal"><span class="pre">indices()</span></tt></a> and it is the user&#8217;s responsibility
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.indices" title="MDAnalysis.core.AtomGroup.AtomGroup.indices"><code class="xref py py-meth docutils literal"><span class="pre">indices()</span></code></a> and it is the user&#8217;s responsibility
 to provide a time step that has the appropriate dimensions.</p>
 </dd>
 <dt><em>copy</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: always make a copy (slow), <tt class="docutils literal"><span class="pre">False</span></tt>: Try to
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: always make a copy (slow), <code class="docutils literal"><span class="pre">False</span></code>: Try to
 return a array view or reference (faster); note that for
 passing coordinates to C-code it can be necessary to use
-a copy [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+a copy [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>dtype</em></dt>
 <dd><p class="first last">NumPy Data type of the array; the default is usually
 entirely appropriate. Most C-code actually requires the
-default  [<tt class="xref py py-class docutils literal"><span class="pre">numpy.float32</span></tt>]</p>
+default  [<code class="xref py py-class docutils literal"><span class="pre">numpy.float32</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -1582,40 +1734,41 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </tbody>
 </table>
 <p>Forces can also be directly obtained from the attribute
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.forces" title="MDAnalysis.core.AtomGroup.AtomGroup.forces"><tt class="xref py py-attr docutils literal"><span class="pre">forces</span></tt></a>.</p>
-<p>Forces can be directly set with <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_forces" title="MDAnalysis.core.AtomGroup.AtomGroup.set_forces"><tt class="xref py py-meth docutils literal"><span class="pre">set_forces()</span></tt></a> or
-by assigning to <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.forces" title="MDAnalysis.core.AtomGroup.AtomGroup.forces"><tt class="xref py py-attr docutils literal"><span class="pre">forces</span></tt></a>.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.forces" title="MDAnalysis.core.AtomGroup.AtomGroup.forces"><code class="xref py py-attr docutils literal"><span class="pre">forces</span></code></a>.</p>
+<p>Forces can be directly set with <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_forces" title="MDAnalysis.core.AtomGroup.AtomGroup.set_forces"><code class="xref py py-meth docutils literal"><span class="pre">set_forces()</span></code></a> or
+by assigning to <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.forces" title="MDAnalysis.core.AtomGroup.AtomGroup.forces"><code class="xref py py-attr docutils literal"><span class="pre">forces</span></code></a>.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.get_positions">
-<tt class="descname">get_positions</tt><big>(</big><em>ts=None</em>, <em>copy=False</em>, <em>dtype=&lt;type 'numpy.float32'&gt;</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.get_positions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_positions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">get_positions</code><span class="sig-paren">(</span><em>ts=None</em>, <em>copy=False</em>, <em>dtype=&lt;type 'numpy.float32'&gt;</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.get_positions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_positions" title="Permalink to this definition">¶</a></dt>
 <dd><p>Get a NumPy array of the coordinates.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>ts</em></dt>
 <dd><p class="first last">If <em>ts</em> is provided then positions are read from that
-<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instead of
+<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instead of
 the one from the current trajectory belonging to this universe.
 The <em>ts</em> is indexed with the indices returned by
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.indices" title="MDAnalysis.core.AtomGroup.AtomGroup.indices"><tt class="xref py py-meth docutils literal"><span class="pre">indices()</span></tt></a> and it is the user&#8217;s responsibility
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.indices" title="MDAnalysis.core.AtomGroup.AtomGroup.indices"><code class="xref py py-meth docutils literal"><span class="pre">indices()</span></code></a> and it is the user&#8217;s responsibility
 to provide a time step that has the appropriate dimensions.</p>
 </dd>
 <dt><em>copy</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: always make a copy (slow), <tt class="docutils literal"><span class="pre">False</span></tt>: Try to
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: always make a copy (slow), <code class="docutils literal"><span class="pre">False</span></code>: Try to
 return a array view or reference (faster); note that for
 passing coordinates to C-code it can be necessary to use
-a copy [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+a copy [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 <dt><em>dtype</em></dt>
 <dd><p class="first last">NumPy Data type of the array; the default is usually
 entirely appropriate. Most C-code actually requires the
-default  [<tt class="xref py py-class docutils literal"><span class="pre">numpy.float32</span></tt>]</p>
+default  [<code class="xref py py-class docutils literal"><span class="pre">numpy.float32</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -1623,37 +1776,39 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </tbody>
 </table>
 <p>Coordinates can also be directly obtained from the attribute
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="MDAnalysis.core.AtomGroup.AtomGroup.positions"><tt class="xref py py-attr docutils literal"><span class="pre">positions</span></tt></a>.</p>
-<p>Coordinates can be directly set with <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.set_positions"><tt class="xref py py-meth docutils literal"><span class="pre">set_positions()</span></tt></a> or
-by assigning to <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="MDAnalysis.core.AtomGroup.AtomGroup.positions"><tt class="xref py py-attr docutils literal"><span class="pre">positions</span></tt></a>.</p>
-<p>This method is identical with <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><tt class="xref py py-meth docutils literal"><span class="pre">coordinates()</span></tt></a> but named
-differently for symmetry with with <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.set_positions"><tt class="xref py py-meth docutils literal"><span class="pre">set_positions()</span></tt></a>.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="MDAnalysis.core.AtomGroup.AtomGroup.positions"><code class="xref py py-attr docutils literal"><span class="pre">positions</span></code></a>.</p>
+<p>Coordinates can be directly set with <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.set_positions"><code class="xref py py-meth docutils literal"><span class="pre">set_positions()</span></code></a> or
+by assigning to <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="MDAnalysis.core.AtomGroup.AtomGroup.positions"><code class="xref py py-attr docutils literal"><span class="pre">positions</span></code></a>.</p>
+<p>This method is identical with <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.coordinates" title="MDAnalysis.core.AtomGroup.AtomGroup.coordinates"><code class="xref py py-meth docutils literal"><span class="pre">coordinates()</span></code></a> but named
+differently for symmetry with with <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.set_positions"><code class="xref py py-meth docutils literal"><span class="pre">set_positions()</span></code></a>.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.get_velocities">
-<tt class="descname">get_velocities</tt><big>(</big><em>ts=None</em>, <em>copy=False</em>, <em>dtype=&lt;type 'numpy.float32'&gt;</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.get_velocities"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_velocities" title="Permalink to this definition">¶</a></dt>
+<code class="descname">get_velocities</code><span class="sig-paren">(</span><em>ts=None</em>, <em>copy=False</em>, <em>dtype=&lt;type 'numpy.float32'&gt;</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.get_velocities"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_velocities" title="Permalink to this definition">¶</a></dt>
 <dd><p>NumPy array of the velocities.</p>
-<p>Raises a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.NoDataError" title="MDAnalysis.core.AtomGroup.NoDataError"><tt class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></tt></a> if the underlying
-<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> does not contain
-<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.velocities" title="MDAnalysis.coordinates.base.Timestep.velocities"><tt class="xref py py-attr docutils literal"><span class="pre">velocities</span></tt></a>.</p>
-<p>See also <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.set_velocities"><tt class="xref py py-meth docutils literal"><span class="pre">AtomGroup.set_velocities()</span></tt></a> and attribute access through
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.velocities"><tt class="xref py py-attr docutils literal"><span class="pre">AtomGroup.velocities</span></tt></a>.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<p>Raises a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.NoDataError" title="MDAnalysis.core.AtomGroup.NoDataError"><code class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></code></a> if the underlying
+<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> does not contain
+<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.velocities" title="MDAnalysis.coordinates.base.Timestep.velocities"><code class="xref py py-attr docutils literal"><span class="pre">velocities</span></code></a>.</p>
+<p>See also <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.set_velocities"><code class="xref py py-meth docutils literal"><span class="pre">AtomGroup.set_velocities()</span></code></a> and attribute access through
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.velocities"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.velocities</span></code></a>.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.guess_bonds">
-<tt class="descname">guess_bonds</tt><big>(</big><em>vdwradii=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.guess_bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.guess_bonds" title="Permalink to this definition">¶</a></dt>
+<code class="descname">guess_bonds</code><span class="sig-paren">(</span><em>vdwradii=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.guess_bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.guess_bonds" title="Permalink to this definition">¶</a></dt>
 <dd><p>Guess all the bonds that exist within this AtomGroup and add to Universe.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>vdwradii</em></dt>
 <dd><p class="first last">Pass a dict relating atom types to vdwradii.</p>
 </dd>
@@ -1662,79 +1817,115 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../topology/core.html#MDAnalysis.topology.core.guess_bonds" title="MDAnalysis.topology.core.guess_bonds"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.core.guess_bonds()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="../topology/core.html#MDAnalysis.topology.core.guess_bonds" title="MDAnalysis.topology.core.guess_bonds"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.core.guess_bonds()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.10.0.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.10.0.</span></p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.improper">
-<tt class="descname">improper</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.improper"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.improper" title="Permalink to this definition">¶</a></dt>
+<code class="descname">improper</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.improper" title="Permalink to this definition">¶</a></dt>
 <dd><p>This AtomGroup represented as an ImproperDihedral object</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">A <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.ImproperDihedral</span></tt> object</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.ImproperDihedral</span></code> object</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><cite>ValueError</cite> if the AtomGroup is not length 4</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><cite>ValueError</cite> if the AtomGroup is not length 4</td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.impropers">
-<tt class="descname">impropers</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.impropers"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.impropers" title="Permalink to this definition">¶</a></dt>
+<code class="descname">impropers</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.impropers" title="Permalink to this definition">¶</a></dt>
 <dd><p>All the improper dihedrals in this AtomGroup</p>
 <p>Note that these improper dihedrals might extend out of the AtomGroup,
 to select only dihedrals which are entirely contained by the AtomGroup use
 u.impropers.atomgroup_intersection(ag, strict=True)</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>Now always returns a (possibly empty) TopologyGroup</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>Now always returns a (possibly empty) TopologyGroup</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.indices">
-<tt class="descname">indices</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.indices"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.indices" title="Permalink to this definition">¶</a></dt>
-<dd><p>Array of all <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.index" title="MDAnalysis.core.AtomGroup.Atom.index"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.index</span></tt></a> in the group.</p>
+<code class="descname">indices</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.indices" title="Permalink to this definition">¶</a></dt>
+<dd><p>Array of all <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.index" title="MDAnalysis.core.AtomGroup.Atom.index"><code class="xref py py-attr docutils literal"><span class="pre">Atom.index</span></code></a> in the group.</p>
 <p>These indices are 0-based and can be used to directly index
-<tt class="xref py py-attr docutils literal"><span class="pre">Universe.atoms</span></tt> or the coordinate array
-<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.positions" title="MDAnalysis.coordinates.base.Timestep.positions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.positions</span></tt></a>.</p>
+<code class="xref py py-attr docutils literal"><span class="pre">Universe.atoms</span></code> or the coordinate array
+<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.positions" title="MDAnalysis.coordinates.base.Timestep.positions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.positions</span></code></a>.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">This property is read only</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.masses">
-<tt class="descname">masses</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.masses"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.masses" title="Permalink to this definition">¶</a></dt>
+<code class="descname">masses</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.masses" title="Permalink to this definition">¶</a></dt>
 <dd><p>Array of atomic masses (as defined in the topology)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.momentOfInertia">
-<tt class="descname">momentOfInertia</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.momentOfInertia"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.momentOfInertia" title="Permalink to this definition">¶</a></dt>
+<code class="descname">momentOfInertia</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.momentOfInertia" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>momentOfInertia</cite> is deprecated, use <cite>moment_of_inertia</cite> instead!</p>
+<p>Tensor of inertia as 3x3 NumPy array.</p>
+<blockquote>
+<div><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>pbc</em></dt>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
+flag to be used by default.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.moment_of_inertia">
+<code class="descname">moment_of_inertia</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.moment_of_inertia"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.moment_of_inertia" title="Permalink to this definition">¶</a></dt>
 <dd><p>Tensor of inertia as 3x3 NumPy array.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>pbc</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: Move all atoms within the primary unit cell before calculation [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -1743,57 +1934,102 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> flag <em>use_pbc</em> when set to <tt class="docutils literal"><span class="pre">True</span></tt> allows the <em>pbc</em>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
 flag to be used by default.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.n_atoms">
-<tt class="descname">n_atoms</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.n_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.n_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_atoms</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.n_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total number of atoms in the group</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.n_residues">
-<tt class="descname">n_residues</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.n_residues"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.n_residues" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_residues</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.n_residues" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total number of residues in the group</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.n_segments">
-<tt class="descname">n_segments</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.n_segments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.n_segments" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_segments</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.n_segments" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total number of segments in the group</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.names">
-<tt class="descname">names</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.names"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.names" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a list of atom names.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+<code class="descname">names</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.names" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an array of atom names.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.packIntoBox">
-<tt class="descname">packIntoBox</tt><big>(</big><em>box=None</em>, <em>inplace=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.packIntoBox"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.packIntoBox" title="Permalink to this definition">¶</a></dt>
+<code class="descname">packIntoBox</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.packIntoBox" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>packIntoBox</cite> is deprecated, use <cite>pack_into_box</cite> instead!</p>
+<p>Shift all atoms in this group to be within the primary unit cell.</p>
+<blockquote>
+<div><p>AtomGroup.packintobox([box, [inplace=True]])</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>box</em></dt>
+<dd><p class="first last">Unit cell to move atoms inside of.</p>
+</dd>
+<dt><em>inplace</em></dt>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Change coordinates in place and return
+<code class="docutils literal"><span class="pre">False</span></code>: Only return the coordinates</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
+<p>All atoms will be moved so that they lie between 0 and
+boxlength <span class="math">\(L_i\)</span> in all dimensions, i.e. the lower left
+corner of the simulation box is taken to be at (0,0,0):</p>
+<div class="math">
+\[x_i' = x_i - \left\lfloor\frac{x_i}{L_i}\right\rfloor\]</div>
+<p>The default is to take unit cell information from the
+underlying <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>
+instance. The optional argument <em>box</em> can be used to provide
+alternative unit cell information (in the MDAnalysis standard
+format <code class="docutils literal"><span class="pre">[Lx,</span> <span class="pre">Ly,</span> <span class="pre">Lz,</span> <span class="pre">alpha,</span> <span class="pre">beta,</span> <span class="pre">gamma]</span></code>).</p>
+<p>Works with either orthogonal or triclinic box types.</p>
+<p>By default the coordinates are changed in place and returned</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.pack_into_box">
+<code class="descname">pack_into_box</code><span class="sig-paren">(</span><em>box=None</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.pack_into_box"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.pack_into_box" title="Permalink to this definition">¶</a></dt>
 <dd><p>Shift all atoms in this group to be within the primary unit cell.</p>
 <p>AtomGroup.packintobox([box, [inplace=True]])</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>box</em></dt>
 <dd><p class="first last">Unit cell to move atoms inside of.</p>
 </dd>
 <dt><em>inplace</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: Change coordinates in place and return
-<tt class="docutils literal"><span class="pre">False</span></tt>: Only return the coordinates</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Change coordinates in place and return
+<code class="docutils literal"><span class="pre">False</span></code>: Only return the coordinates</p>
 </dd>
 </dl>
 </td>
@@ -1806,44 +2042,88 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <div class="math">
 \[x_i' = x_i - \left\lfloor\frac{x_i}{L_i}\right\rfloor\]</div>
 <p>The default is to take unit cell information from the
-underlying <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>
+underlying <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>
 instance. The optional argument <em>box</em> can be used to provide
 alternative unit cell information (in the MDAnalysis standard
-format <tt class="docutils literal"><span class="pre">[Lx,</span> <span class="pre">Ly,</span> <span class="pre">Lz,</span> <span class="pre">alpha,</span> <span class="pre">beta,</span> <span class="pre">gamma]</span></tt>).</p>
+format <code class="docutils literal"><span class="pre">[Lx,</span> <span class="pre">Ly,</span> <span class="pre">Lz,</span> <span class="pre">alpha,</span> <span class="pre">beta,</span> <span class="pre">gamma]</span></code>).</p>
 <p>Works with either orthogonal or triclinic box types.</p>
 <p>By default the coordinates are changed in place and returned</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.positions">
-<tt class="descname">positions</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">positions</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="Permalink to this definition">¶</a></dt>
 <dd><p>Coordinates of the atoms in the AtomGroup.</p>
 <p>The positions can be changed by assigning an array of the appropriate
 shape, i.e. either Nx3 to assign individual coordinates or 3, to assign
-the <em>same</em> coordinate to all atoms (e.g. <tt class="docutils literal"><span class="pre">ag.positions</span> <span class="pre">=</span> <span class="pre">array([0,0,0])</span></tt>
+the <em>same</em> coordinate to all atoms (e.g. <code class="docutils literal"><span class="pre">ag.positions</span> <span class="pre">=</span> <span class="pre">array([0,0,0])</span></code>
 will move all particles to the origin).</p>
-<p>For more control use the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.get_positions"><tt class="xref py py-meth docutils literal"><span class="pre">get_positions()</span></tt></a> and
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.set_positions"><tt class="xref py py-meth docutils literal"><span class="pre">set_positions()</span></tt></a> methods.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<p>For more control use the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.get_positions"><code class="xref py py-meth docutils literal"><span class="pre">get_positions()</span></code></a> and
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.set_positions"><code class="xref py py-meth docutils literal"><span class="pre">set_positions()</span></code></a> methods.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.principalAxes">
-<tt class="descname">principalAxes</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.principalAxes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.principalAxes" title="Permalink to this definition">¶</a></dt>
+<code class="descname">principalAxes</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.principalAxes" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>principalAxes</cite> is deprecated, use <cite>principal_axes</cite> instead!</p>
+<p>Calculate the principal axes from the moment of inertia.</p>
+<blockquote>
+<div><p>e1,e2,e3 = AtomGroup.principal_axes()</p>
+<p>The eigenvectors are sorted by eigenvalue, i.e. the first one
+corresponds to the highest eigenvalue and is thus the first principal axes.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>pbc</em></dt>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within primary unit cell before calculation</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
+flag to be used by default.</p>
+</div>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">numpy.array <code class="docutils literal"><span class="pre">v</span></code> with <code class="docutils literal"><span class="pre">v[0]</span></code> as first, <code class="docutils literal"><span class="pre">v[1]</span></code> as second,
+and <code class="docutils literal"><span class="pre">v[2]</span></code> as third eigenvector.</td>
+</tr>
+</tbody>
+</table>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.principal_axes">
+<code class="descname">principal_axes</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.principal_axes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.principal_axes" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate the principal axes from the moment of inertia.</p>
-<p>e1,e2,e3 = AtomGroup.principalAxes()</p>
+<p>e1,e2,e3 = AtomGroup.principal_axes()</p>
 <p>The eigenvectors are sorted by eigenvalue, i.e. the first one
 corresponds to the highest eigenvalue and is thus the first principal axes.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>pbc</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: Move all atoms within primary unit cell before calculation</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within primary unit cell before calculation</p>
 </dd>
 </dl>
 </td>
@@ -1852,41 +2132,73 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> flag <em>use_pbc</em> when set to <tt class="docutils literal"><span class="pre">True</span></tt> allows the <em>pbc</em>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
 flag to be used by default.</p>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">numpy.array <tt class="docutils literal"><span class="pre">v</span></tt> with <tt class="docutils literal"><span class="pre">v[0]</span></tt> as first, <tt class="docutils literal"><span class="pre">v[1]</span></tt> as second,
-and <tt class="docutils literal"><span class="pre">v[2]</span></tt> as third eigenvector.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">numpy.array <code class="docutils literal"><span class="pre">v</span></code> with <code class="docutils literal"><span class="pre">v[0]</span></code> as first, <code class="docutils literal"><span class="pre">v[1]</span></code> as second,
+and <code class="docutils literal"><span class="pre">v[2]</span></code> as third eigenvector.</td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.radii">
-<tt class="descname">radii</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.radii"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.radii" title="Permalink to this definition">¶</a></dt>
+<code class="descname">radii</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.radii" title="Permalink to this definition">¶</a></dt>
 <dd><p>Array of atomic radii (as defined in the PQR file)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.radiusOfGyration">
-<tt class="descname">radiusOfGyration</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.radiusOfGyration"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.radiusOfGyration" title="Permalink to this definition">¶</a></dt>
+<code class="descname">radiusOfGyration</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.radiusOfGyration" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>radiusOfGyration</cite> is deprecated, use <cite>radius_of_gyration</cite> instead!</p>
+<p>Radius of gyration.</p>
+<blockquote>
+<div><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>pbc</em></dt>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
+flag to be used by default.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.radius_of_gyration">
+<code class="descname">radius_of_gyration</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.radius_of_gyration"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.radius_of_gyration" title="Permalink to this definition">¶</a></dt>
 <dd><p>Radius of gyration.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>pbc</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: Move all atoms within the primary unit cell before calculation [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -1895,59 +2207,68 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> flag <em>use_pbc</em> when set to <tt class="docutils literal"><span class="pre">True</span></tt> allows the <em>pbc</em>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
 flag to be used by default.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.resids">
-<tt class="descname">resids</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.resids"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.resids" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a list of residue numbers.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+<code class="descname">resids</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.resids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an array of residue numbers.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property and returns array of length <cite>len(self)</cite></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.residues">
-<tt class="descname">residues</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.residues"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="Permalink to this definition">¶</a></dt>
-<dd><p>Read-only list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> objects.</p>
-<p>A <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a> of all residues that contain atoms in
+<code class="descname">residues</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="Permalink to this definition">¶</a></dt>
+<dd><p>Read-only list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> objects.</p>
+<p>A <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a> of all residues that contain atoms in
 this group.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Now returns strictly a ResidueGroup of the unique Residues that Atoms in this group
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Now returns strictly a ResidueGroup of the unique Residues that Atoms in this group
 belong to.</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.resnames">
-<tt class="descname">resnames</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.resnames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.resnames" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a list of residue names.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+<code class="descname">resnames</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.resnames" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an array of residue names.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property and returns array of length <cite>len(self)</cite></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.resnums">
-<tt class="descname">resnums</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.resnums"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.resnums" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a list of canonical residue numbers.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+<code class="descname">resnums</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.resnums" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an array of canonical residue numbers.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property and returns array of length <cite>len(self)</cite></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.rotate">
-<tt class="descname">rotate</tt><big>(</big><em>R</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.rotate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.rotate" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rotate</code><span class="sig-paren">(</span><em>R</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.rotate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.rotate" title="Permalink to this definition">¶</a></dt>
 <dd><p>Apply a rotation matrix <em>R</em> to the selection&#8217;s coordinates.</p>
 <p>AtomGroup.rotate(R)</p>
 <p><span class="math">\(\mathsf{R}\)</span> is a 3x3 orthogonal matrix that transforms a vector
@@ -1958,7 +2279,7 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.rotateby">
-<tt class="descname">rotateby</tt><big>(</big><em>angle</em>, <em>axis</em>, <em>point=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.rotateby"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.rotateby" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rotateby</code><span class="sig-paren">(</span><em>angle</em>, <em>axis</em>, <em>point=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.rotateby"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.rotateby" title="Permalink to this definition">¶</a></dt>
 <dd><p>Apply a rotation to the selection&#8217;s coordinates.</p>
 <p>AtomGroup.rotateby(angle,axis[,point])</p>
 <p>The transformation from current coordinates <span class="math">\(\mathbf{x}\)</span>
@@ -1971,7 +2292,7 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>angle</em></dt>
 <dd><p class="first last">rotation angle in degrees</p>
 </dd>
@@ -1981,17 +2302,17 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 vector from the first to the second center of geometry.</p>
 </dd>
 <dt><em>point</em></dt>
-<dd><p class="first last">point on the rotation axis; by default (<tt class="docutils literal"><span class="pre">None</span></tt>) the center of
+<dd><p class="first last">point on the rotation axis; by default (<code class="docutils literal"><span class="pre">None</span></code>) the center of
 geometry of the selection is chosen, or, if <em>axis</em> is a tuple of
 selections, it defaults to the first point of the axis. <em>point</em>
 can be a 3-tuple, list, or array or a MDAnalysis object (in which
-case its <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.centroid" title="MDAnalysis.core.AtomGroup.AtomGroup.centroid"><tt class="xref py py-meth docutils literal"><span class="pre">centroid()</span></tt></a> is used).</p>
+case its <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.centroid" title="MDAnalysis.core.AtomGroup.AtomGroup.centroid"><code class="xref py py-meth docutils literal"><span class="pre">centroid()</span></code></a> is used).</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">The 4x4 matrix which consists of the rotation matrix <tt class="docutils literal"><span class="pre">M[:3,:3]</span></tt>
-and the translation vector <tt class="docutils literal"><span class="pre">M[:3,3]</span></tt>.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The 4x4 matrix which consists of the rotation matrix <code class="docutils literal"><span class="pre">M[:3,:3]</span></code>
+and the translation vector <code class="docutils literal"><span class="pre">M[:3,3]</span></code>.</p>
 </td>
 </tr>
 </tbody>
@@ -2000,52 +2321,55 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.segids">
-<tt class="descname">segids</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.segids"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.segids" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a list of segment ids (=segment names).</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+<code class="descname">segids</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.segids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an array of segment names.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property and returns array of length <cite>len(self)</cite></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.segments">
-<tt class="descname">segments</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.segments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.segments" title="Permalink to this definition">¶</a></dt>
-<dd><p>Read-only list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a> objects.</p>
-<p>A <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></a> of all segments that contain atoms in this group.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Now strictly returns a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></a> of a set of
-the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a> instances from this <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></p>
+<code class="descname">segments</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.segments" title="Permalink to this definition">¶</a></dt>
+<dd><p>Read-only list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></a> objects.</p>
+<p>A <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code></a> of all segments that contain atoms in this group.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Now strictly returns a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code></a> of a set of
+the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></a> instances from this <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.selectAtoms">
-<tt class="descname">selectAtoms</tt><big>(</big><em>*args</em>, <em>**kwds</em><big>)</big><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.selectAtoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">selectAtoms</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.selectAtoms" title="Permalink to this definition">¶</a></dt>
 <dd><p><cite>selectAtoms</cite> is deprecated, use <cite>select_atoms</cite> instead!</p>
 <p>Selection of atoms using the MDAnalysis selection syntax.</p>
 <blockquote>
 <div><p>AtomGroup.select_atoms(selection[,selection[,...]], [groupname=atomgroup[,groupname=atomgroup[,...]]])</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">Universe.select_atoms()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">Universe.select_atoms()</span></code></a></p>
 </div>
 </div></blockquote>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms">
-<tt class="descname">select_atoms</tt><big>(</big><em>sel</em>, <em>*othersel</em>, <em>**selgroups</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.select_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">select_atoms</code><span class="sig-paren">(</span><em>sel</em>, <em>*othersel</em>, <em>**selgroups</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.select_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Selection of atoms using the MDAnalysis selection syntax.</p>
 <p>AtomGroup.select_atoms(selection[,selection[,...]], [groupname=atomgroup[,groupname=atomgroup[,...]]])</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">Universe.select_atoms()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">Universe.select_atoms()</span></code></a></p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.sequence">
-<tt class="descname">sequence</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.sequence"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.sequence" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sequence</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.sequence"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.sequence" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns the amino acid sequence.</p>
 <p>The format of the sequence is selected with the keyword <em>format</em>:</p>
 <table border="1" class="docutils">
@@ -2060,29 +2384,29 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </thead>
 <tbody valign="top">
 <tr class="row-even"><td>&#8216;SeqRecord&#8217;</td>
-<td><tt class="xref py py-class docutils literal"><span class="pre">Bio.SeqRecord.SeqRecord</span></tt> (default)</td>
+<td><code class="xref py py-class docutils literal"><span class="pre">Bio.SeqRecord.SeqRecord</span></code> (default)</td>
 </tr>
 <tr class="row-odd"><td>&#8216;Seq&#8217;</td>
-<td><tt class="xref py py-class docutils literal"><span class="pre">Bio.Seq.Seq</span></tt></td>
+<td><code class="xref py py-class docutils literal"><span class="pre">Bio.Seq.Seq</span></code></td>
 </tr>
 <tr class="row-even"><td>&#8216;string&#8217;</td>
 <td>string</td>
 </tr>
 </tbody>
 </table>
-<p>The sequence is returned by default (keyword <tt class="docutils literal"><span class="pre">format</span> <span class="pre">=</span> <span class="pre">'SeqRecord'</span></tt>)
-as a <tt class="xref py py-class docutils literal"><span class="pre">Bio.SeqRecord.SeqRecord</span></tt> instance, which can then be
+<p>The sequence is returned by default (keyword <code class="docutils literal"><span class="pre">format</span> <span class="pre">=</span> <span class="pre">'SeqRecord'</span></code>)
+as a <code class="xref py py-class docutils literal"><span class="pre">Bio.SeqRecord.SeqRecord</span></code> instance, which can then be
 further processed. In this case, all keyword arguments (such as the
 <em>id</em> string or the <em>name</em> or the <em>description</em>) are directly passed to
-<tt class="xref py py-class docutils literal"><span class="pre">Bio.SeqRecord.SeqRecord</span></tt>.</p>
-<p>If the keyword <em>format</em> is set to <tt class="docutils literal"><span class="pre">'Seq'</span></tt>, all <em>kwargs</em> are ignored
-and a <tt class="xref py py-class docutils literal"><span class="pre">Bio.Seq.Seq</span></tt> instance is returned. The difference to the
+<code class="xref py py-class docutils literal"><span class="pre">Bio.SeqRecord.SeqRecord</span></code>.</p>
+<p>If the keyword <em>format</em> is set to <code class="docutils literal"><span class="pre">'Seq'</span></code>, all <em>kwargs</em> are ignored
+and a <code class="xref py py-class docutils literal"><span class="pre">Bio.Seq.Seq</span></code> instance is returned. The difference to the
 record is that the record also contains metadata and can be directly
-used as an input for other functions in <tt class="xref py py-mod docutils literal"><span class="pre">Bio</span></tt>.</p>
-<p>If the keyword <em>format</em> is set to <tt class="docutils literal"><span class="pre">'string'</span></tt>, all <em>kwargs</em> are
+used as an input for other functions in <code class="xref py py-mod docutils literal"><span class="pre">Bio</span></code>.</p>
+<p>If the keyword <em>format</em> is set to <code class="docutils literal"><span class="pre">'string'</span></code>, all <em>kwargs</em> are
 ignored and a Python string is returned.</p>
 <p class="rubric">Example: Write FASTA file</p>
-<p>Use <tt class="xref py py-func docutils literal"><span class="pre">Bio.SeqIO.write()</span></tt>, which takes sequence records:</p>
+<p>Use <code class="xref py py-func docutils literal"><span class="pre">Bio.SeqIO.write()</span></code>, which takes sequence records:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">Bio.SeqIO</span>
 
 <span class="c"># get the sequence record of a protein component of a Universe</span>
@@ -2100,16 +2424,16 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><p class="first"><em>format</em></p>
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><p class="first"><em>format</em></p>
 <blockquote>
 <div><blockquote>
 <div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">&quot;string&quot;</span></tt>: return sequence as a string of 1-letter codes</li>
-<li><tt class="docutils literal"><span class="pre">&quot;Seq&quot;</span></tt>: return a <tt class="xref py py-class docutils literal"><span class="pre">Bio.Seq.Seq</span></tt> instance</li>
-<li><tt class="docutils literal"><span class="pre">&quot;SeqRecord&quot;</span></tt>: return a <tt class="xref py py-class docutils literal"><span class="pre">Bio.SeqRecord.SeqRecord</span></tt>
+<li><code class="docutils literal"><span class="pre">&quot;string&quot;</span></code>: return sequence as a string of 1-letter codes</li>
+<li><code class="docutils literal"><span class="pre">&quot;Seq&quot;</span></code>: return a <code class="xref py py-class docutils literal"><span class="pre">Bio.Seq.Seq</span></code> instance</li>
+<li><code class="docutils literal"><span class="pre">&quot;SeqRecord&quot;</span></code>: return a <code class="xref py py-class docutils literal"><span class="pre">Bio.SeqRecord.SeqRecord</span></code>
 instance</li>
 </ul>
-<p>Default is <tt class="docutils literal"><span class="pre">&quot;SeqRecord&quot;</span></tt></p>
+<p>Default is <code class="docutils literal"><span class="pre">&quot;SeqRecord&quot;</span></code></p>
 </div></blockquote>
 <dl class="docutils">
 <dt><em>id</em></dt>
@@ -2124,96 +2448,181 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </dd>
 <dt><em>kwargs</em></dt>
 <dd><p class="first last">Any other keyword arguments that are understood by
-<tt class="xref py py-class docutils literal"><span class="pre">Bio.SeqRecord.SeqRecord</span></tt>.</p>
+<code class="xref py py-class docutils literal"><span class="pre">Bio.SeqRecord.SeqRecord</span></code>.</p>
 </dd>
 </dl>
 </div></blockquote>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><p class="first last"><tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> if a residue name cannot be converted to a
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> if a residue name cannot be converted to a
 1-letter IUPAC protein amino acid code; make sure to only
-select protein residues. Raises <tt class="xref py py-exc docutils literal"><span class="pre">TypeError</span></tt> if an unknown
+select protein residues. Raises <code class="xref py py-exc docutils literal"><span class="pre">TypeError</span></code> if an unknown
 <em>format</em> is selected.</p>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.serials">
-<tt class="descname">serials</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.serials"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.serials" title="Permalink to this definition">¶</a></dt>
+<code class="descname">serials</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.serials" title="Permalink to this definition">¶</a></dt>
 <dd><p>numpy array of the serials for all atoms in this group</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set">
-<tt class="descname">set</tt><big>(</big><em>name</em>, <em>value</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set attribute <em>name</em> to <em>value</em> for all atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>.</p>
-<p>If <em>value</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
-then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>&#8216;s property <em>name</em> is set to the corresponding value. If
+<code class="descname">set</code><span class="sig-paren">(</span><em>name</em>, <em>value</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set attribute <em>name</em> to <em>value</em> for all atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
+<p>If <em>value</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>&#8216;s property <em>name</em> is set to the corresponding value. If
 <em>value</em> is neither of length 1 (or a scalar) nor of the length of the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms to distinct values by providing a sequence or iterable.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms to distinct values by providing a sequence or iterable.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_altLoc">
-<tt class="descname">set_altLoc</tt><big>(</big><em>altLoc</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_altLoc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_altLoc" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the altLoc of atoms in this group</p>
-<p>This can apply a single value to all atoms, or a series of
-values to each atom</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<code class="descname">set_altLoc</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_altLoc" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_altLoc</cite> is deprecated, use <cite>set_altLocs</cite> instead!</p>
+<p>Set the altLocs to <em>altLoc for **all atoms*</em> in the AtomGroup.</p>
+<blockquote>
+<div><p>If <em>altLoc</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.altLoc" title="MDAnalysis.core.AtomGroup.Atom.altLoc"><code class="xref py py-attr docutils literal"><span class="pre">Atom.altLoc</span></code></a> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_altLocs">
+<code class="descname">set_altLocs</code><span class="sig-paren">(</span><em>altLoc</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_altLocs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_altLocs" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the altLocs to <em>altLoc for **all atoms*</em> in the AtomGroup.</p>
+<p>If <em>altLoc</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.altLoc" title="MDAnalysis.core.AtomGroup.Atom.altLoc"><code class="xref py py-attr docutils literal"><span class="pre">Atom.altLoc</span></code></a> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_bfactor">
-<tt class="descname">set_bfactor</tt><big>(</big><em>bfactor</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_bfactor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_bfactor" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the atom bfactor to float <em>bfactor</em> for <strong>all atoms</strong> in the AtomGroup.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+<code class="descname">set_bfactor</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_bfactor" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_bfactor</cite> is deprecated, use <cite>set_bfactors</cite> instead!</p>
+<p>Set the atom bfactors to float <em>bfactor</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<blockquote>
+<div><p>If <em>bfactor</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <code class="xref py py-attr docutils literal"><span class="pre">Atom.bfactor</span></code> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_bfactors">
+<code class="descname">set_bfactors</code><span class="sig-paren">(</span><em>bfactor</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_bfactors"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_bfactors" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the atom bfactors to float <em>bfactor</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<p>If <em>bfactor</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <code class="xref py py-attr docutils literal"><span class="pre">Atom.bfactor</span></code> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_charge">
-<tt class="descname">set_charge</tt><big>(</big><em>charge</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_charge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_charge" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the partial charge to float <em>charge</em> for <strong>all atoms</strong> in the AtomGroup.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+<code class="descname">set_charge</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_charge" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_charge</cite> is deprecated, use <cite>set_charges</cite> instead!</p>
+<p>Set the partial charges to float <em>charge</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<blockquote>
+<div><p>If <em>charge</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.charge" title="MDAnalysis.core.AtomGroup.Atom.charge"><code class="xref py py-attr docutils literal"><span class="pre">Atom.charge</span></code></a> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_charges">
+<code class="descname">set_charges</code><span class="sig-paren">(</span><em>charge</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_charges"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_charges" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the partial charges to float <em>charge</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<p>If <em>charge</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.charge" title="MDAnalysis.core.AtomGroup.Atom.charge"><code class="xref py py-attr docutils literal"><span class="pre">Atom.charge</span></code></a> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_forces">
-<tt class="descname">set_forces</tt><big>(</big><em>forces</em>, <em>ts=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_forces"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_forces" title="Permalink to this definition">¶</a></dt>
+<code class="descname">set_forces</code><span class="sig-paren">(</span><em>forces</em>, <em>ts=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_forces"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_forces" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set the forces for all atoms in the group.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>forces</em></dt>
-<dd><p class="first last">a Nx3 NumPy <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> where N is the number of
+<dd><p class="first last">a Nx3 NumPy <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> where N is the number of
 atoms in this atom group.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>ts</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>, defaults
-to <tt class="docutils literal"><span class="pre">None</span></tt> and then the current time step is used.</p>
+<dd><p class="first last"><a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>, defaults
+to <code class="docutils literal"><span class="pre">None</span></code> and then the current time step is used.</p>
 </dd>
 </dl>
 </td>
@@ -2225,58 +2634,117 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <p class="last">If the group contains N atoms and <em>force</em> is a single vector (i.e. an
 array of length 3) then all N atom positions are set to <em>force</em> (due
 to NumPy&#8217;s broadcasting rules), as described for
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.forces" title="MDAnalysis.core.AtomGroup.AtomGroup.forces"><tt class="xref py py-attr docutils literal"><span class="pre">forces</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.forces" title="MDAnalysis.core.AtomGroup.AtomGroup.forces"><code class="xref py py-attr docutils literal"><span class="pre">forces</span></code></a>.</p>
+</div>
+<p>See also <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_forces" title="MDAnalysis.core.AtomGroup.AtomGroup.get_forces"><code class="xref py py-meth docutils literal"><span class="pre">get_forces()</span></code></a> and attribute access through
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.forces" title="MDAnalysis.core.AtomGroup.AtomGroup.forces"><code class="xref py py-attr docutils literal"><span class="pre">forces</span></code></a>.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
 </div>
-<p>See also <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_forces" title="MDAnalysis.core.AtomGroup.AtomGroup.get_forces"><tt class="xref py py-meth docutils literal"><span class="pre">get_forces()</span></tt></a> and attribute access through
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.forces" title="MDAnalysis.core.AtomGroup.AtomGroup.forces"><tt class="xref py py-attr docutils literal"><span class="pre">forces</span></tt></a>.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_mass">
-<tt class="descname">set_mass</tt><big>(</big><em>mass</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_mass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_mass" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the atom mass to float <em>mass</em> for <strong>all atoms</strong> in the AtomGroup.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+<code class="descname">set_mass</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_mass" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_mass</cite> is deprecated, use <cite>set_masses</cite> instead!</p>
+<p>Set the atom masses to float <em>mass</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<blockquote>
+<div><p>If <em>mass</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.mass" title="MDAnalysis.core.AtomGroup.Atom.mass"><code class="xref py py-attr docutils literal"><span class="pre">Atom.mass</span></code></a> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_masses">
+<code class="descname">set_masses</code><span class="sig-paren">(</span><em>mass</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_masses"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_masses" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the atom masses to float <em>mass</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<p>If <em>mass</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.mass" title="MDAnalysis.core.AtomGroup.Atom.mass"><code class="xref py py-attr docutils literal"><span class="pre">Atom.mass</span></code></a> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_name">
-<tt class="descname">set_name</tt><big>(</big><em>name</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_name"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_name" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the atom name to string for <em>all atoms</em> in the AtomGroup.</p>
-<p>If <em>value</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
-then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.name" title="MDAnalysis.core.AtomGroup.Atom.name"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.name</span></tt></a> is set to the corresponding value. If
+<code class="descname">set_name</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_name" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_name</cite> is deprecated, use <cite>set_names</cite> instead!</p>
+<p>Set the atom names to string for <em>all atoms</em> in the AtomGroup.</p>
+<blockquote>
+<div><p>If <em>value</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.name" title="MDAnalysis.core.AtomGroup.Atom.name"><code class="xref py py-attr docutils literal"><span class="pre">Atom.name</span></code></a> is set to the corresponding value. If
 <em>value</em> is neither of length 1 (or a scalar) nor of the length of the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms to distinct values by providing a sequence or iterable.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_names">
+<code class="descname">set_names</code><span class="sig-paren">(</span><em>name</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_names"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_names" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the atom names to string for <em>all atoms</em> in the AtomGroup.</p>
+<p>If <em>value</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.name" title="MDAnalysis.core.AtomGroup.Atom.name"><code class="xref py py-attr docutils literal"><span class="pre">Atom.name</span></code></a> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_positions">
-<tt class="descname">set_positions</tt><big>(</big><em>coords</em>, <em>ts=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_positions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_positions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">set_positions</code><span class="sig-paren">(</span><em>coords</em>, <em>ts=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_positions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_positions" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set the positions for all atoms in the group.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>coords</em></dt>
-<dd><p class="first last">a Nx3 NumPy <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> where N is the number of
+<dd><p class="first last">a Nx3 NumPy <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> where N is the number of
 atoms in this atom group.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>ts</em></dt>
-<dd><p class="first last"><a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a>, defaults
-to <tt class="docutils literal"><span class="pre">None</span></tt> and then the current time step is used.</p>
+<dd><p class="first last"><a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a>, defaults
+to <code class="docutils literal"><span class="pre">None</span></code> and then the current time step is used.</p>
 </dd>
 </dl>
 </td>
@@ -2288,33 +2756,67 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <p class="last">If the group contains N atoms and <em>coord</em> is a single point (i.e. an
 array of length 3) then all N atom positions are set to <em>coord</em> (due
 to NumPy&#8217;s broadcasting rules), as described for
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="MDAnalysis.core.AtomGroup.AtomGroup.positions"><tt class="xref py py-attr docutils literal"><span class="pre">positions</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="MDAnalysis.core.AtomGroup.AtomGroup.positions"><code class="xref py py-attr docutils literal"><span class="pre">positions</span></code></a>.</p>
+</div>
+<p>See also <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.get_positions"><code class="xref py py-meth docutils literal"><span class="pre">get_positions()</span></code></a> and attribute access through
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="MDAnalysis.core.AtomGroup.AtomGroup.positions"><code class="xref py py-attr docutils literal"><span class="pre">positions</span></code></a>.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_radii">
+<code class="descname">set_radii</code><span class="sig-paren">(</span><em>radius</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_radii"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_radii" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the atom radii to float <em>radius</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<p>If <em>radius</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.radius" title="MDAnalysis.core.AtomGroup.Atom.radius"><code class="xref py py-attr docutils literal"><span class="pre">Atom.radius</span></code></a> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
 </div>
-<p>See also <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_positions" title="MDAnalysis.core.AtomGroup.AtomGroup.get_positions"><tt class="xref py py-meth docutils literal"><span class="pre">get_positions()</span></tt></a> and attribute access through
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.positions" title="MDAnalysis.core.AtomGroup.AtomGroup.positions"><tt class="xref py py-attr docutils literal"><span class="pre">positions</span></tt></a>.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_radius">
-<tt class="descname">set_radius</tt><big>(</big><em>radius</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_radius"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_radius" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the atom radius to float <em>radius</em> for <strong>all atoms</strong> in the AtomGroup.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+<code class="descname">set_radius</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_radius" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_radius</cite> is deprecated, use <cite>set_radii</cite> instead!</p>
+<p>Set the atom radii to float <em>radius</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<blockquote>
+<div><p>If <em>radius</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.radius" title="MDAnalysis.core.AtomGroup.Atom.radius"><code class="xref py py-attr docutils literal"><span class="pre">Atom.radius</span></code></a> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_resid">
-<tt class="descname">set_resid</tt><big>(</big><em>resid</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_resid"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resid" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the resid to integer <em>resid</em> for <strong>all atoms</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>.</p>
-<p>If <em>resid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
-then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="MDAnalysis.core.AtomGroup.Atom.resid"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.resid</span></tt></a> is set to the corresponding value together
-with the <tt class="xref py py-attr docutils literal"><span class="pre">Residue.id</span></tt> of the residue the atom belongs to. If
+<code class="descname">set_resid</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resid" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_resid</cite> is deprecated, use <cite>set_resids</cite> instead!</p>
+<p>Set the resids to integer <em>resid</em> for <strong>all atoms</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
+<blockquote>
+<div><p>If <em>resid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="MDAnalysis.core.AtomGroup.Atom.resid"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resid</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.id</span></code> of the residue the atom belongs to. If
 <em>value</em> is neither of length 1 (or a scalar) nor of the length of the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p>Changing resids can change the topology.</p>
@@ -2323,131 +2825,361 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 atoms in the same residue will <strong>split</strong> a residue (and
 potentially merge with another one).</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a
 sequence or iterable and can change the topology via
-<a class="reference internal" href="../topology/core.html#MDAnalysis.topology.core.build_residues" title="MDAnalysis.topology.core.build_residues"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.core.build_residues()</span></tt></a>.</p>
+<a class="reference internal" href="../topology/core.html#MDAnalysis.topology.core.build_residues" title="MDAnalysis.topology.core.build_residues"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.core.build_residues()</span></code></a>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_resids">
+<code class="descname">set_resids</code><span class="sig-paren">(</span><em>resid</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_resids"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the resids to integer <em>resid</em> for <strong>all atoms</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
+<p>If <em>resid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="MDAnalysis.core.AtomGroup.Atom.resid"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resid</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.id</span></code> of the residue the atom belongs to. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p>Changing resids can change the topology.</p>
+<p class="last">Assigning the same <em>resid</em> to multiple residues will
+<strong>merge</strong> these residues. Assigning different <em>resid</em> to
+atoms in the same residue will <strong>split</strong> a residue (and
+potentially merge with another one).</p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a
+sequence or iterable and can change the topology via
+<a class="reference internal" href="../topology/core.html#MDAnalysis.topology.core.build_residues" title="MDAnalysis.topology.core.build_residues"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.core.build_residues()</span></code></a>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_resname">
-<tt class="descname">set_resname</tt><big>(</big><em>resname</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_resname"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resname" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the resname to string <em>resname</em> for <strong>all atoms</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>.</p>
-<p>If <em>resname</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
-then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resname" title="MDAnalysis.core.AtomGroup.Atom.resname"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.resname</span></tt></a> is set to the corresponding value together
-with the <tt class="xref py py-attr docutils literal"><span class="pre">Residue.name</span></tt> of the residue the atom belongs to. If
+<code class="descname">set_resname</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resname" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_resname</cite> is deprecated, use <cite>set_resnames</cite> instead!</p>
+<p>Set the resnames to string <em>resname</em> for <strong>all atoms</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
+<blockquote>
+<div><p>If <em>resname</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resname" title="MDAnalysis.core.AtomGroup.Atom.resname"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resname</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.name</span></code> of the residue the atom belongs to. If
 <em>value</em> is neither of length 1 (or a scalar) nor of the length of the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_resnames">
+<code class="descname">set_resnames</code><span class="sig-paren">(</span><em>resname</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_resnames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resnames" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the resnames to string <em>resname</em> for <strong>all atoms</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
+<p>If <em>resname</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resname" title="MDAnalysis.core.AtomGroup.Atom.resname"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resname</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.name</span></code> of the residue the atom belongs to. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_resnum">
-<tt class="descname">set_resnum</tt><big>(</big><em>resnum</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_resnum"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resnum" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the resnum to <em>resnum</em> for <strong>all atoms</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>.</p>
-<p>If <em>resnum</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
-then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resnum" title="MDAnalysis.core.AtomGroup.Atom.resnum"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.resnum</span></tt></a> is set to the corresponding value together
-with the <tt class="xref py py-attr docutils literal"><span class="pre">Residue.resnum</span></tt> of the residue the atom belongs to. If
+<code class="descname">set_resnum</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resnum" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_resnum</cite> is deprecated, use <cite>set_resnums</cite> instead!</p>
+<p>Set the resnums to <em>resnum</em> for <strong>all atoms</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
+<blockquote>
+<div><p>If <em>resnum</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resnum" title="MDAnalysis.core.AtomGroup.Atom.resnum"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resnum</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.resnum</span></code> of the residue the atom belongs to. If
 <em>value</em> is neither of length 1 (or a scalar) nor of the length of the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">Changing <em>resnum</em> will not affect the topology: you can have
 multiple residues with the same <em>resnum</em>.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resid" title="MDAnalysis.core.AtomGroup.AtomGroup.set_resid"><tt class="xref py py-meth docutils literal"><span class="pre">set_resid()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resid" title="MDAnalysis.core.AtomGroup.AtomGroup.set_resid"><code class="xref py py-meth docutils literal"><span class="pre">set_resid()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_resnums">
+<code class="descname">set_resnums</code><span class="sig-paren">(</span><em>resnum</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_resnums"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resnums" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the resnums to <em>resnum</em> for <strong>all atoms</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
+<p>If <em>resnum</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resnum" title="MDAnalysis.core.AtomGroup.Atom.resnum"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resnum</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.resnum</span></code> of the residue the atom belongs to. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">Changing <em>resnum</em> will not affect the topology: you can have
+multiple residues with the same <em>resnum</em>.</p>
+</div>
+<div class="admonition seealso">
+<p class="first admonition-title">See also</p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_resid" title="MDAnalysis.core.AtomGroup.AtomGroup.set_resid"><code class="xref py py-meth docutils literal"><span class="pre">set_resid()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_segid">
-<tt class="descname">set_segid</tt><big>(</big><em>segid</em>, <em>buildsegments=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_segid"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_segid" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the segid to <em>segid</em> for all atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>.</p>
-<p>If <em>segid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>
-then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.segid</span></tt></a> is set to the corresponding value together
-with the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment.id" title="MDAnalysis.core.AtomGroup.Segment.id"><tt class="xref py py-attr docutils literal"><span class="pre">Segment.id</span></tt></a> of the residue the atom belongs to. If
+<code class="descname">set_segid</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_segid" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_segid</cite> is deprecated, use <cite>set_segids</cite> instead!</p>
+<p>Set the segids to <em>segid</em> for all atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
+<blockquote>
+<div><p>If <em>segid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><code class="xref py py-attr docutils literal"><span class="pre">Atom.segid</span></code></a> is set to the corresponding value together
+with the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment.id" title="MDAnalysis.core.AtomGroup.Segment.id"><code class="xref py py-attr docutils literal"><span class="pre">Segment.id</span></code></a> of the residue the atom belongs to. If
 <em>value</em> is neither of length 1 (or a scalar) nor of the length of the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_segid" title="MDAnalysis.core.AtomGroup.AtomGroup.set_segid"><tt class="xref py py-meth docutils literal"><span class="pre">set_segid()</span></tt></a> can change the topology.</p>
-<p class="last">With the default <em>buildsegments</em> = <tt class="docutils literal"><span class="pre">True</span></tt> it can be used to join
-segments or to break groups into multiple disjoint segments. Note
-that each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> can only belong to a single
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a>.</p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_segid" title="MDAnalysis.core.AtomGroup.AtomGroup.set_segid"><code class="xref py py-meth docutils literal"><span class="pre">set_segid()</span></code></a> can change the topology.</p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Stale caches are problematic; though it can be expensive, changing segid
+results in Segments being regenerated</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_segids">
+<code class="descname">set_segids</code><span class="sig-paren">(</span><em>segid</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_segids"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_segids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the segids to <em>segid</em> for all atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
+<p>If <em>segid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><code class="xref py py-attr docutils literal"><span class="pre">Atom.segid</span></code></a> is set to the corresponding value together
+with the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment.id" title="MDAnalysis.core.AtomGroup.Segment.id"><code class="xref py py-attr docutils literal"><span class="pre">Segment.id</span></code></a> of the residue the atom belongs to. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_segid" title="MDAnalysis.core.AtomGroup.AtomGroup.set_segid"><code class="xref py py-meth docutils literal"><span class="pre">set_segid()</span></code></a> can change the topology.</p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Stale caches are problematic; though it can be expensive, changing segid
+results in Segments being regenerated</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
 </div>
-<p>For performance reasons, <em>buildsegments</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt>. Then
-one needs to run <tt class="xref py py-meth docutils literal"><span class="pre">Universe._build_segments()</span></tt> manually later in
-order to update the list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a> instances and regenerate
-the segid instant selectors.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_serial">
-<tt class="descname">set_serial</tt><big>(</big><em>serial</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_serial"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_serial" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the serial of atoms in this group</p>
-<p>This can apply a single value to all atoms, or a series of
-values to each atom</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<code class="descname">set_serial</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_serial" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_serial</cite> is deprecated, use <cite>set_serials</cite> instead!</p>
+<p>Set the serials to <em>serial</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<blockquote>
+<div><p>If <em>serial</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <code class="xref py py-attr docutils literal"><span class="pre">Atom.serial</span></code> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_serials">
+<code class="descname">set_serials</code><span class="sig-paren">(</span><em>serial</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_serials"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_serials" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the serials to <em>serial</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<p>If <em>serial</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <code class="xref py py-attr docutils literal"><span class="pre">Atom.serial</span></code> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_type">
-<tt class="descname">set_type</tt><big>(</big><em>atype</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_type"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_type" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the atom type to <em>atype</em> for <strong>all atoms</strong> in the AtomGroup.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+<code class="descname">set_type</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_type" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_type</cite> is deprecated, use <cite>set_types</cite> instead!</p>
+<p>Set the atom types to <em>atype</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<blockquote>
+<div><p>If <em>atype</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <code class="xref py py-attr docutils literal"><span class="pre">Atom.atype</span></code> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_types">
+<code class="descname">set_types</code><span class="sig-paren">(</span><em>atype</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_types"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_types" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the atom types to <em>atype</em> for <strong>all atoms</strong> in the AtomGroup.</p>
+<p>If <em>atype</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>
+then each <code class="xref py py-attr docutils literal"><span class="pre">Atom.atype</span></code> is set to the corresponding value. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.set_velocities">
-<tt class="descname">set_velocities</tt><big>(</big><em>v</em>, <em>ts=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_velocities"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_velocities" title="Permalink to this definition">¶</a></dt>
+<code class="descname">set_velocities</code><span class="sig-paren">(</span><em>v</em>, <em>ts=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.set_velocities"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_velocities" title="Permalink to this definition">¶</a></dt>
 <dd><p>Assign the velocities <em>v</em> to the timestep.</p>
-<p>Raises a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.NoDataError" title="MDAnalysis.core.AtomGroup.NoDataError"><tt class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></tt></a> if the underlying
-<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> does not contain
-<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.velocities" title="MDAnalysis.coordinates.base.Timestep.velocities"><tt class="xref py py-attr docutils literal"><span class="pre">velocities</span></tt></a>.</p>
-<p>See also <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.get_velocities"><tt class="xref py py-meth docutils literal"><span class="pre">AtomGroup.get_velocities()</span></tt></a> and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.velocities"><tt class="xref py py-attr docutils literal"><span class="pre">AtomGroup.velocities</span></tt></a> for
+<p>Raises a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.NoDataError" title="MDAnalysis.core.AtomGroup.NoDataError"><code class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></code></a> if the underlying
+<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> does not contain
+<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.velocities" title="MDAnalysis.coordinates.base.Timestep.velocities"><code class="xref py py-attr docutils literal"><span class="pre">velocities</span></code></a>.</p>
+<p>See also <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.get_velocities"><code class="xref py py-meth docutils literal"><span class="pre">AtomGroup.get_velocities()</span></code></a> and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.velocities"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.velocities</span></code></a> for
 attribute access.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.6.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.6.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.shapeParameter">
-<tt class="descname">shapeParameter</tt><big>(</big><em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.shapeParameter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.shapeParameter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">shapeParameter</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.shapeParameter" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>shapeParameter</cite> is deprecated, use <cite>shape_parameter</cite> instead!</p>
+<p>Shape parameter.</p>
+<blockquote>
+<div><p>See <a class="reference internal" href="#dima2004" id="id4">[Dima2004]</a> for background information.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>pbc</em></dt>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
+flag to be used by default.</p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.shape_parameter">
+<code class="descname">shape_parameter</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.shape_parameter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.shape_parameter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Shape parameter.</p>
-<p>See <a class="reference internal" href="#dima2004">[Dima2004]</a> for background information.</p>
+<p>See <a class="reference internal" href="#dima2004" id="id5">[Dima2004]</a> for background information.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>pbc</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt>: Move all atoms within the primary unit cell before calculation [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">True</span></code>: Move all atoms within the primary unit cell before calculation [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -2456,42 +3188,57 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt> flag <em>use_pbc</em> when set to <tt class="docutils literal"><span class="pre">True</span></tt> allows the <em>pbc</em>
+<p class="last">The <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.flags</span></code> flag <em>use_pbc</em> when set to <code class="docutils literal"><span class="pre">True</span></code> allows the <em>pbc</em>
 flag to be used by default.</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Added <em>pbc</em> keyword</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.split">
-<tt class="descname">split</tt><big>(</big><em>level</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.split"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.split" title="Permalink to this definition">¶</a></dt>
+<code class="descname">split</code><span class="sig-paren">(</span><em>level</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.split"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.split" title="Permalink to this definition">¶</a></dt>
 <dd><p>Split atomgroup into a list of atomgroups by <em>level</em>.</p>
-<p><em>level</em> can be &#8220;atom&#8221;, &#8220;residue&#8221;, &#8220;segment&#8221;.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
+<p><em>level</em> can be &#8220;atom&#8221;, &#8220;residue&#8221;, &#8220;segment&#8221;.
+.. versionadded:: 0.9.0</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.totalCharge">
-<tt class="descname">totalCharge</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.totalCharge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.totalCharge" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sum of all partial charges (must be defined in topology).</p>
+<code class="descname">totalCharge</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.totalCharge" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>totalCharge</cite> is deprecated, use <cite>total_charge</cite> instead!</p>
+<p>Sum of all partial charges (must be defined in topology).</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.totalMass">
-<tt class="descname">totalMass</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.totalMass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.totalMass" title="Permalink to this definition">¶</a></dt>
+<code class="descname">totalMass</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.totalMass" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>totalMass</cite> is deprecated, use <cite>total_mass</cite> instead!</p>
+<p>Total mass of the selection (masses are taken from the topology or guessed).</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.total_charge">
+<code class="descname">total_charge</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.total_charge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.total_charge" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sum of all partial charges (must be defined in topology).</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.AtomGroup.total_mass">
+<code class="descname">total_mass</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.total_mass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.total_mass" title="Permalink to this definition">¶</a></dt>
 <dd><p>Total mass of the selection (masses are taken from the topology or guessed).</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.transform">
-<tt class="descname">transform</tt><big>(</big><em>M</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.transform"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.transform" title="Permalink to this definition">¶</a></dt>
+<code class="descname">transform</code><span class="sig-paren">(</span><em>M</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.transform"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.transform" title="Permalink to this definition">¶</a></dt>
 <dd><p>Apply homogenous transformation matrix <em>M</em> to the coordinates.</p>
 <p>The matrix <em>M</em> must be a 4x4 matrix, with the rotation in
-<cite>R = `M[:3,:3]`</cite> and the translation in <tt class="docutils literal"><span class="pre">t</span> <span class="pre">=</span> <span class="pre">M[:3,3]</span></tt>.</p>
+<cite>R = `M[:3,:3]`</cite> and the translation in <code class="docutils literal"><span class="pre">t</span> <span class="pre">=</span> <span class="pre">M[:3,3]</span></code>.</p>
 <p>The rotation <span class="math">\(\mathsf{R}\)</span> is applied before the
 translation <span class="math">\(\mathbf{t}\)</span>:</p>
 <div class="math">
@@ -2500,7 +3247,7 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.translate">
-<tt class="descname">translate</tt><big>(</big><em>t</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.translate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.translate" title="Permalink to this definition">¶</a></dt>
+<code class="descname">translate</code><span class="sig-paren">(</span><em>t</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.translate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.translate" title="Permalink to this definition">¶</a></dt>
 <dd><p>Apply translation vector <em>t</em> to the selection&#8217;s coordinates.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">AtomGroup</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">AtomGroup</span><span class="o">.</span><span class="n">translate</span><span class="p">((</span><span class="n">A</span><span class="p">,</span> <span class="n">B</span><span class="p">))</span>
@@ -2511,8 +3258,8 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <div class="math">
 \[\mathbf{x}' = \mathbf{x} + \mathbf{t}\]</div>
 <p>The translation can also be given as a tuple of two MDAnalysis objects
-such as two selections <cite>(selA, selB)</cite>, i.e. two <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>, or
-two <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>. The translation vector is computed as the
+such as two selections <cite>(selA, selB)</cite>, i.e. two <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>, or
+two <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>. The translation vector is computed as the
 difference between the centers of geometry (centroid) of B and A:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">t</span> <span class="o">=</span> <span class="n">B</span><span class="o">.</span><span class="n">centroid</span><span class="p">()</span> <span class="o">-</span> <span class="n">A</span><span class="o">.</span><span class="n">centroid</span><span class="p">()</span>
 </pre></div>
@@ -2521,77 +3268,82 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.ts">
-<tt class="descname">ts</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.ts"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.ts" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ts</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.ts" title="Permalink to this definition">¶</a></dt>
 <dd><p>Temporary Timestep that contains the selection coordinates.</p>
-<p>A <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> instance,
+<p>A <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> instance,
 which can be passed to a trajectory writer.</p>
-<p>If <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.ts" title="MDAnalysis.core.AtomGroup.AtomGroup.ts"><tt class="xref py py-attr docutils literal"><span class="pre">ts</span></tt></a> is modified then these modifications
+<p>If <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.ts" title="MDAnalysis.core.AtomGroup.AtomGroup.ts"><code class="xref py py-attr docutils literal"><span class="pre">ts</span></code></a> is modified then these modifications
 will be present until the frame number changes (which
 typically happens when the underlying trajectory frame
 changes).</p>
 <p>It is not possible to assign a new
-<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt></a> to the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.ts" title="MDAnalysis.core.AtomGroup.AtomGroup.ts"><tt class="xref py py-attr docutils literal"><span class="pre">AtomGroup.ts</span></tt></a> attribute; change attributes of the object.</p>
+<a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep" title="MDAnalysis.coordinates.base.Timestep"><code class="xref py py-class docutils literal"><span class="pre">Timestep</span></code></a> to the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.ts" title="MDAnalysis.core.AtomGroup.AtomGroup.ts"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.ts</span></code></a> attribute; change attributes of the object.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.types">
-<tt class="descname">types</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.types"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.types" title="Permalink to this definition">¶</a></dt>
+<code class="descname">types</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.types" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns an array of atom types.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.universe">
-<tt class="descname">universe</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.universe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.universe" title="Permalink to this definition">¶</a></dt>
+<code class="descname">universe</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.universe" title="Permalink to this definition">¶</a></dt>
 <dd><p>The universe to which the atoms belong (read-only).</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.velocities">
-<tt class="descname">velocities</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.velocities" title="Permalink to this definition">¶</a></dt>
+<code class="descname">velocities</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.velocities" title="Permalink to this definition">¶</a></dt>
 <dd><p>NumPy array of the velocities of the atoms in the group.</p>
 <p>If the trajectory does not contain velocity information then a
-<tt class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></tt> is raised.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
-<p class="deprecated">
-<span class="versionmodified">Deprecated since version 0.7.6: </span>In 0.8 this will become an attribute! You can already use <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.get_velocities"><tt class="xref py py-meth docutils literal"><span class="pre">get_velocities()</span></tt></a>
-and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.set_velocities"><tt class="xref py py-meth docutils literal"><span class="pre">set_velocities()</span></tt></a>.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Became an attribute.</p>
+<code class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
+<div class="deprecated">
+<p><span class="versionmodified">Deprecated since version 0.7.6: </span>In 0.8 this will become an attribute! You can already use <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.get_velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.get_velocities"><code class="xref py py-meth docutils literal"><span class="pre">get_velocities()</span></code></a>
+and <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.set_velocities" title="MDAnalysis.core.AtomGroup.AtomGroup.set_velocities"><code class="xref py py-meth docutils literal"><span class="pre">set_velocities()</span></code></a>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Became an attribute.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.wrap">
-<tt class="descname">wrap</tt><big>(</big><em>compound='atoms'</em>, <em>center='com'</em>, <em>box=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.wrap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.wrap" title="Permalink to this definition">¶</a></dt>
+<code class="descname">wrap</code><span class="sig-paren">(</span><em>compound='atoms'</em>, <em>center='com'</em>, <em>box=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.wrap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.wrap" title="Permalink to this definition">¶</a></dt>
 <dd><p>Shift the contents of this AtomGroup back into the unit cell.</p>
-<p>This is a more powerful version of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.packIntoBox" title="MDAnalysis.core.AtomGroup.AtomGroup.packIntoBox"><tt class="xref py py-meth docutils literal"><span class="pre">packIntoBox()</span></tt></a>, allowing
+<p>This is a more powerful version of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.pack_into_box" title="MDAnalysis.core.AtomGroup.AtomGroup.pack_into_box"><code class="xref py py-meth docutils literal"><span class="pre">pack_into_box()</span></code></a>, allowing
 groups of atoms to be kept together through the process.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>compound</em></dt>
 <dd><p class="first">The group which will be kept together through the shifting
-process. [<tt class="docutils literal"><span class="pre">atoms</span></tt>]</p>
+process. [<code class="docutils literal"><span class="pre">atoms</span></code>]</p>
 <p>Possible options:</p>
 <blockquote class="last">
 <div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">atoms</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">group</span></tt> - This AtomGroup</li>
-<li><tt class="docutils literal"><span class="pre">residues</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">segments</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">fragments</span></tt></li>
+<li><code class="docutils literal"><span class="pre">atoms</span></code></li>
+<li><code class="docutils literal"><span class="pre">group</span></code> - This AtomGroup</li>
+<li><code class="docutils literal"><span class="pre">residues</span></code></li>
+<li><code class="docutils literal"><span class="pre">segments</span></code></li>
+<li><code class="docutils literal"><span class="pre">fragments</span></code></li>
 </ul>
 </div></blockquote>
 </dd>
 <dt><em>center</em></dt>
-<dd><p class="first last">How to define the center of a given group of atoms [<tt class="docutils literal"><span class="pre">com</span></tt>]</p>
+<dd><p class="first last">How to define the center of a given group of atoms [<code class="docutils literal"><span class="pre">com</span></code>]</p>
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">Unit cell information.  If not provided, the values from
@@ -2617,24 +3369,25 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 will be used.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">wrap with all default keywords is identical to <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.packIntoBox" title="MDAnalysis.core.AtomGroup.AtomGroup.packIntoBox"><tt class="xref py py-meth docutils literal"><span class="pre">packIntoBox()</span></tt></a></p>
+<p class="last">wrap with all default keywords is identical to <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.pack_into_box" title="MDAnalysis.core.AtomGroup.AtomGroup.pack_into_box"><code class="xref py py-meth docutils literal"><span class="pre">pack_into_box()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.2.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.2.</span></p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.write">
-<tt class="descname">write</tt><big>(</big><em>filename=None</em>, <em>format='PDB'</em>, <em>filenamefmt='%(trjname)s_%(frame)d'</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>filename=None</em>, <em>format='PDB'</em>, <em>filenamefmt='%(trjname)s_%(frame)d'</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write AtomGroup to a file.</p>
 <p>AtomGroup.write(filename[,format])</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">None</span></tt>: create TRJNAME_FRAME.FORMAT from filenamefmt [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">None</span></code>: create TRJNAME_FRAME.FORMAT from filenamefmt [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>format</em></dt>
 <dd><p class="first last">PDB, CRD, GRO, VMD (tcl), PyMol (pml), Gromacs (ndx) CHARMM (str)
@@ -2647,13 +3400,13 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </dd>
 <dt><em>bonds</em></dt>
 <dd><p class="first">how to handle bond information, especially relevant for PDBs;
-default is <tt class="docutils literal"><span class="pre">&quot;conect&quot;</span></tt>.</p>
+default is <code class="docutils literal"><span class="pre">&quot;conect&quot;</span></code>.</p>
 <ul class="last simple">
-<li><tt class="docutils literal"><span class="pre">&quot;conect&quot;</span></tt>: write only the CONECT records defined in the original
+<li><code class="docutils literal"><span class="pre">&quot;conect&quot;</span></code>: write only the CONECT records defined in the original
 file</li>
-<li><tt class="docutils literal"><span class="pre">&quot;all&quot;</span></tt>: write out all bonds, both the original defined and those
+<li><code class="docutils literal"><span class="pre">&quot;all&quot;</span></code>: write out all bonds, both the original defined and those
 guessed by MDAnalysis</li>
-<li><tt class="docutils literal"><span class="pre">None</span></tt>: do not write out bonds</li>
+<li><code class="docutils literal"><span class="pre">None</span></code>: do not write out bonds</li>
 </ul>
 </dd>
 </dl>
@@ -2661,22 +3414,23 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Merged with write_selection.  This method can now write both
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Merged with write_selection.  This method can now write both
 selections out.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.AtomGroup.write_selection">
-<tt class="descname">write_selection</tt><big>(</big><em>filename=None</em>, <em>format='vmd'</em>, <em>filenamefmt='%(trjname)s_%(frame)d'</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.write_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.write_selection" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_selection</code><span class="sig-paren">(</span><em>filename=None</em>, <em>format='vmd'</em>, <em>filenamefmt='%(trjname)s_%(frame)d'</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#AtomGroup.write_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.AtomGroup.write_selection" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write AtomGroup selection to a file to be used in another programme.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">None</span></tt>: create TRJNAME_FRAME.FORMAT from <em>filenamefmt</em></p>
+<dd><p class="first last"><code class="docutils literal"><span class="pre">None</span></code>: create TRJNAME_FRAME.FORMAT from <em>filenamefmt</em></p>
 </dd>
 <dt><em>format</em></dt>
 <dd><p class="first last">output file format: VMD (tcl), PyMol (pml), Gromacs (ndx), CHARMM (str);
@@ -2689,263 +3443,280 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </dd>
 <dt><em>kwargs</em></dt>
 <dd><p class="first last">additional keywords are passed on to the appropriate
-<a class="reference internal" href="../selections/base.html#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><tt class="xref py py-class docutils literal"><span class="pre">SelectionWriter</span></tt></a></p>
+<a class="reference internal" href="../selections/base.html#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><code class="xref py py-class docutils literal"><span class="pre">SelectionWriter</span></code></a></p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="deprecated">
-<span class="versionmodified">Deprecated since version 0.9.0: </span>Use <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.write" title="MDAnalysis.core.AtomGroup.AtomGroup.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a></p>
+<div class="deprecated">
+<p><span class="versionmodified">Deprecated since version 0.9.0: </span>Use <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.write" title="MDAnalysis.core.AtomGroup.AtomGroup.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a></p>
+</div>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.AtomGroup.Atom">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">Atom</tt><big>(</big><em>index</em>, <em>name</em>, <em>type</em>, <em>resname</em>, <em>resid</em>, <em>segid</em>, <em>mass</em>, <em>charge</em>, <em>residue=None</em>, <em>segment=None</em>, <em>radius=None</em>, <em>bfactor=None</em>, <em>resnum=None</em>, <em>serial=None</em>, <em>altLoc=None</em>, <em>universe=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">Atom</code><span class="sig-paren">(</span><em>index</em>, <em>name</em>, <em>type</em>, <em>resname</em>, <em>resid</em>, <em>segid</em>, <em>mass</em>, <em>charge</em>, <em>residue=None</em>, <em>segment=None</em>, <em>radius=None</em>, <em>bfactor=None</em>, <em>resnum=None</em>, <em>serial=None</em>, <em>altLoc=None</em>, <em>universe=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom" title="Permalink to this definition">¶</a></dt>
 <dd><p>A class representing a single atom.</p>
-<p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> is the basic building block of all larger data
+<p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> is the basic building block of all larger data
 structures in MDAnalysis, in particular of the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>.</p>
-<p>An <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> is typically generated by a <a class="reference internal" href="../topology/init.html#supported-topology-formats"><em>topology reader</em></a> from <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology</span></tt>.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
+<p>An <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> is typically generated by a <a class="reference internal" href="../topology/init.html#supported-topology-formats"><span>topology reader</span></a> from <code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology</span></code>.</p>
 <p>For performance reasons, only a predefined number of attributes
 are included (and thus it is not possible to add attributes &#8220;on
 the fly&#8221;; they have to be included in the class definition).</p>
-<p>An <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> is bound to a particular <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>, but
-via a weak reference only. This means that the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>, and
-any <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> it is in, are only relevant while the
-originating <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> is in scope.</p>
+<p>An <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> is bound to a particular <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>, but
+via a weak reference only. This means that the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>, and
+any <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> it is in, are only relevant while the
+originating <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> is in scope.</p>
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.index">
-<tt class="descname">index</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.index" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.index" title="Permalink to this definition">¶</a></dt>
 <dd><p>atom index</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.segid">
-<tt class="descname">segid</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.segid" title="Permalink to this definition">¶</a></dt>
+<code class="descname">segid</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.segid" title="Permalink to this definition">¶</a></dt>
 <dd><p>name of the segment</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.resid">
-<tt class="descname">resid</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="Permalink to this definition">¶</a></dt>
+<code class="descname">resid</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="Permalink to this definition">¶</a></dt>
 <dd><p>residue number</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.resnum">
-<tt class="descname">resnum</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.resnum" title="Permalink to this definition">¶</a></dt>
+<code class="descname">resnum</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.resnum" title="Permalink to this definition">¶</a></dt>
 <dd><p>canonical residue number as, for instance, used in the original
 PDB file</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.resname">
-<tt class="descname">resname</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.resname" title="Permalink to this definition">¶</a></dt>
+<code class="descname">resname</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.resname" title="Permalink to this definition">¶</a></dt>
 <dd><p>residue name</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.residue">
-<tt class="descname">residue</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.residue" title="Permalink to this definition">¶</a></dt>
-<dd><p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> object containing the atoms</p>
+<code class="descname">residue</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.residue" title="Permalink to this definition">¶</a></dt>
+<dd><p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> object containing the atoms</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.id">
-<tt class="descname">id</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.id" title="Permalink to this definition">¶</a></dt>
+<code class="descname">id</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.id" title="Permalink to this definition">¶</a></dt>
 <dd><p>atom number inside the residue</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.name">
-<tt class="descname">name</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.name" title="Permalink to this definition">¶</a></dt>
+<code class="descname">name</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.name" title="Permalink to this definition">¶</a></dt>
 <dd><p>string, short name</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.type">
-<tt class="descname">type</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.type" title="Permalink to this definition">¶</a></dt>
+<code class="descname">type</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.type" title="Permalink to this definition">¶</a></dt>
 <dd><p>string or number (from force field), describing the atom type;
 stored as a string.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>The <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.type" title="MDAnalysis.core.AtomGroup.Atom.type"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.type</span></tt></a> attribute is always stored as a string.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>The <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.type" title="MDAnalysis.core.AtomGroup.Atom.type"><code class="xref py py-attr docutils literal"><span class="pre">Atom.type</span></code></a> attribute is always stored as a string.</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.mass">
-<tt class="descname">mass</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.mass" title="Permalink to this definition">¶</a></dt>
+<code class="descname">mass</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.mass" title="Permalink to this definition">¶</a></dt>
 <dd><p>float, in <a class="reference external" href="http://physics.nist.gov/cgi-bin/cuu/Value?u">atomic mass units</a> (u)</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.charge">
-<tt class="descname">charge</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.charge" title="Permalink to this definition">¶</a></dt>
+<code class="descname">charge</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.charge" title="Permalink to this definition">¶</a></dt>
 <dd><p>float, in <a class="reference external" href="http://physics.nist.gov/cgi-bin/cuu/Value?e">electron charges</a> (<em>e</em>)</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.radius">
-<tt class="descname">radius</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.radius" title="Permalink to this definition">¶</a></dt>
+<code class="descname">radius</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.radius" title="Permalink to this definition">¶</a></dt>
 <dd><p>Born-radius for electrostatic calculations. (Only if read from a
 PQR file with the
-<a class="reference internal" href="../coordinates/PQR.html#MDAnalysis.coordinates.PQR.PQRReader" title="MDAnalysis.coordinates.PQR.PQRReader"><tt class="xref py py-class docutils literal"><span class="pre">PQRReader</span></tt></a>.)</p>
+<a class="reference internal" href="../coordinates/PQR.html#MDAnalysis.coordinates.PQR.PQRReader" title="MDAnalysis.coordinates.PQR.PQRReader"><code class="xref py py-class docutils literal"><span class="pre">PQRReader</span></code></a>.)</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.altLoc">
-<tt class="descname">altLoc</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.altLoc" title="Permalink to this definition">¶</a></dt>
+<code class="descname">altLoc</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.altLoc" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alternate location indicator (as used in <cite>ATOM_</cite> records in PDB
 files)</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.bonds">
-<tt class="descname">bonds</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.bonds" title="Permalink to this definition">¶</a></dt>
-<dd><p>A <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.TopologyGroup</span></tt> of all
-<tt class="xref py py-class docutils literal"><span class="pre">Bond</span></tt> instances that
+<code class="descname">bonds</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.bonds" title="Permalink to this definition">¶</a></dt>
+<dd><p>A <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.TopologyGroup</span></code> of all
+<code class="xref py py-class docutils literal"><span class="pre">Bond</span></code> instances that
 contains all the bonds that this atom participates in.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.1.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.1.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.angles">
-<tt class="descname">angles</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.angles"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.angles" title="Permalink to this definition">¶</a></dt>
-<dd><p>A <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.TopologyGroup</span></tt> of all
-<tt class="xref py py-class docutils literal"><span class="pre">Angle</span></tt> instances
+<code class="descname">angles</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.angles" title="Permalink to this definition">¶</a></dt>
+<dd><p>A <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.TopologyGroup</span></code> of all
+<code class="xref py py-class docutils literal"><span class="pre">Angle</span></code> instances
 that contains all the angles that this atom participates in.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.1.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.1.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.dihedrals">
-<tt class="descname">dihedrals</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.dihedrals"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.dihedrals" title="Permalink to this definition">¶</a></dt>
-<dd><p>A <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.TopologyGroup</span></tt> of all
-<tt class="xref py py-class docutils literal"><span class="pre">Dihedral</span></tt> instances
+<code class="descname">dihedrals</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.dihedrals" title="Permalink to this definition">¶</a></dt>
+<dd><p>A <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.TopologyGroup</span></code> of all
+<code class="xref py py-class docutils literal"><span class="pre">Dihedral</span></code> instances
 that contains all the dihedrals that this atom
 participates in.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.1.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.1.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.impropers">
-<tt class="descname">impropers</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.impropers"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.impropers" title="Permalink to this definition">¶</a></dt>
-<dd><p>A <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.TopologyGroup</span></tt> of all
-<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.ImproperDihedral</span></tt> instances
+<code class="descname">impropers</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.impropers" title="Permalink to this definition">¶</a></dt>
+<dd><p>A <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.TopologyGroup</span></code> of all
+<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.topologyobjects.ImproperDihedral</span></code> instances
 that this atom is present in.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.1.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.1.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt>
-<tt class="descname">angles</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.angles"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">angles</code></dt>
 <dd><p>A TopologyGroup of the angles that this Atom is in</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Changed to managed property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Changed to managed property</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.bonded_atoms">
-<tt class="descname">bonded_atoms</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.bonded_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.bonded_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bonded_atoms</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.bonded_atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>An AtomGroup of the Atoms that this Atom is bonded to.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt>
-<tt class="descname">bonds</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.bonds"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">bonds</code></dt>
 <dd><p>A TopologyGroup of the bonds that this Atom is in</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Changed to managed property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Changed to managed property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.Atom.centroid">
-<tt class="descname">centroid</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.centroid"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.centroid" title="Permalink to this definition">¶</a></dt>
-<dd><p>The centroid of an atom is its position, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.position" title="MDAnalysis.core.AtomGroup.Atom.position"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.position</span></tt></a>.</p>
+<code class="descname">centroid</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.centroid"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.centroid" title="Permalink to this definition">¶</a></dt>
+<dd><p>The centroid of an atom is its position, <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.position" title="MDAnalysis.core.AtomGroup.Atom.position"><code class="xref py py-attr docutils literal"><span class="pre">Atom.position</span></code></a>.</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt>
-<tt class="descname">dihedrals</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.dihedrals"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">dihedrals</code></dt>
 <dd><p>A TopologyGroup of the dihedrals that this Atom is in</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Changed to managed property</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Renamed to dihedrals (was torsions)</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Changed to managed property</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Renamed to dihedrals (was torsions)</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.force">
-<tt class="descname">force</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.force"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.force" title="Permalink to this definition">¶</a></dt>
+<code class="descname">force</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.force" title="Permalink to this definition">¶</a></dt>
 <dd><p>Current force of the atom.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">a (3,) shape numpy array</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">a (3,) shape numpy array</td>
 </tr>
 </tbody>
 </table>
-<p>A <tt class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></tt> is raised if the trajectory
+<p>A <code class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></code> is raised if the trajectory
 does not contain velocities.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.2.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.2.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.fragment">
-<tt class="descname">fragment</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.fragment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.fragment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">fragment</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.fragment" title="Permalink to this definition">¶</a></dt>
 <dd><p>The fragment that this Atom is part of</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt>
-<tt class="descname">impropers</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.impropers"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descname">impropers</code></dt>
 <dd><p>A TopologyGroup of the improper dihedrals that this Atom is in</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Changed to managed property</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Changed to managed property</p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.number">
-<tt class="descname">number</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.number"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.number" title="Permalink to this definition">¶</a></dt>
+<code class="descname">number</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.number" title="Permalink to this definition">¶</a></dt>
 <dd><p>The index of this atom</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.pos">
-<tt class="descname">pos</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.pos"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.pos" title="Permalink to this definition">¶</a></dt>
+<code class="descname">pos</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.pos" title="Permalink to this definition">¶</a></dt>
 <dd><p>coordinates of the atom</p>
 <p>Get the current cartesian coordinates of the atom (read-only).</p>
-<p class="deprecated">
-<span class="versionmodified">Deprecated since version 0.8: </span>use <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.position" title="MDAnalysis.core.AtomGroup.Atom.position"><tt class="xref py py-attr docutils literal"><span class="pre">position</span></tt></a></p>
+<div class="deprecated">
+<p><span class="versionmodified">Deprecated since version 0.8: </span>use <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.position" title="MDAnalysis.core.AtomGroup.Atom.position"><code class="xref py py-attr docutils literal"><span class="pre">position</span></code></a></p>
+</div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.position">
-<tt class="descname">position</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.position"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.position" title="Permalink to this definition">¶</a></dt>
+<code class="descname">position</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.position" title="Permalink to this definition">¶</a></dt>
 <dd><p>coordinates of the atom</p>
 <p>Get the current cartesian coordinates of the atom.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">a (3,) shape numpy array</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">a (3,) shape numpy array</td>
 </tr>
 </tbody>
 </table>
@@ -2953,39 +3724,40 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.universe">
-<tt class="descname">universe</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.universe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.universe" title="Permalink to this definition">¶</a></dt>
+<code class="descname">universe</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.universe" title="Permalink to this definition">¶</a></dt>
 <dd><p>a pointer back to the Universe</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Atom.velocity">
-<tt class="descname">velocity</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Atom.velocity"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.velocity" title="Permalink to this definition">¶</a></dt>
+<code class="descname">velocity</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Atom.velocity" title="Permalink to this definition">¶</a></dt>
 <dd><p>Current velocity of the atom.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">a (3,) shape numpy array</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">a (3,) shape numpy array</td>
 </tr>
 </tbody>
 </table>
-<p>A <tt class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></tt> is raised if the trajectory
+<p>A <code class="xref py py-exc docutils literal"><span class="pre">NoDataError</span></code> is raised if the trajectory
 does not contain velocities.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.AtomGroup.Residue">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">Residue</tt><big>(</big><em>name</em>, <em>id</em>, <em>atoms</em>, <em>resnum=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Residue"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Residue" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">Residue</code><span class="sig-paren">(</span><em>name</em>, <em>id</em>, <em>atoms</em>, <em>resnum=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Residue"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Residue" title="Permalink to this definition">¶</a></dt>
 <dd><p>A group of atoms corresponding to a residue.</p>
 <dl class="docutils">
 <dt>Pythonic access to atoms:</dt>
 <dd><ul class="first last">
 <li><p class="first">Using a atom name as attribute returns the matching atom (a
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instance), i.e. <tt class="docutils literal"><span class="pre">r.name</span></tt>. Example:</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instance), i.e. <code class="docutils literal"><span class="pre">r.name</span></code>. Example:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">MDAnalysis.tests.datafiles</span> <span class="kn">import</span> <span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">u</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="k">print</span><span class="p">(</span><span class="n">u</span><span class="o">.</span><span class="n">s4AKE</span><span class="o">.</span><span class="n">r1</span><span class="o">.</span><span class="n">CA</span><span class="p">)</span>  <span class="c"># C-alpha of M1</span>
@@ -2993,7 +3765,7 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </pre></div>
 </div>
 </li>
-<li><p class="first"><tt class="docutils literal"><span class="pre">r['name']</span></tt> or <tt class="docutils literal"><span class="pre">r[id]</span></tt> - returns the atom corresponding to that name</p>
+<li><p class="first"><code class="docutils literal"><span class="pre">r['name']</span></code> or <code class="docutils literal"><span class="pre">r[id]</span></code> - returns the atom corresponding to that name</p>
 </li>
 </ul>
 </dd>
@@ -3002,14 +3774,14 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Data :</th><td class="field-body"><dl class="first last docutils">
-<dt><tt class="xref py py-attr docutils literal"><span class="pre">Residue.name</span></tt></dt>
+<tr class="field-odd field"><th class="field-name">Data:</th><td class="field-body"><dl class="first last docutils">
+<dt><code class="xref py py-attr docutils literal"><span class="pre">Residue.name</span></code></dt>
 <dd><p class="first last">Three letter residue name.</p>
 </dd>
-<dt><tt class="xref py py-attr docutils literal"><span class="pre">Residue.id</span></tt></dt>
+<dt><code class="xref py py-attr docutils literal"><span class="pre">Residue.id</span></code></dt>
 <dd><p class="first last">Numeric (integer) resid, taken from the topology.</p>
 </dd>
-<dt><tt class="xref py py-attr docutils literal"><span class="pre">Residue.resnum</span></tt></dt>
+<dt><code class="xref py py-attr docutils literal"><span class="pre">Residue.resnum</span></code></dt>
 <dd><p class="first last">Numeric canonical residue id (e.g. as used in the PDB structure).</p>
 </dd>
 </dl>
@@ -3019,32 +3791,34 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">Creating a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> modifies the underlying <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>
-instances. Each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> can only belong to a single
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a>.</p>
+<p class="last">Creating a <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> modifies the underlying <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>
+instances. Each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> can only belong to a single
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a>.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.4: </span>Added <code class="xref py py-attr docutils literal"><span class="pre">Residue.resnum</span></code> attribute and <em>resnum</em> keyword argument.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.4: </span>Added <tt class="xref py py-attr docutils literal"><span class="pre">Residue.resnum</span></tt> attribute and <em>resnum</em> keyword argument.</p>
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.Residue.chi1_selection">
-<tt class="descname">chi1_selection</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Residue.chi1_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Residue.chi1_selection" title="Permalink to this definition">¶</a></dt>
+<code class="descname">chi1_selection</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Residue.chi1_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Residue.chi1_selection" title="Permalink to this definition">¶</a></dt>
 <dd><p>AtomGroup corresponding to the chi1 sidechain dihedral N-CA-CB-CG.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">4-atom selection in the correct order.  If no CB and/or CG is
-found then this method returns <tt class="docutils literal"><span class="pre">None</span></tt>.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">4-atom selection in the correct order.  If no CB and/or CG is
+found then this method returns <code class="docutils literal"><span class="pre">None</span></code>.</td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.Residue.omega_selection">
-<tt class="descname">omega_selection</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Residue.omega_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Residue.omega_selection" title="Permalink to this definition">¶</a></dt>
+<code class="descname">omega_selection</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Residue.omega_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Residue.omega_selection" title="Permalink to this definition">¶</a></dt>
 <dd><p>AtomGroup corresponding to the omega protein backbone dihedral CA-C-N&#8217;-CA&#8217;.</p>
 <p>omega describes the -C-N- peptide bond. Typically, it is trans
 (180 degrees) although cis-bonds (0 degrees) are also
@@ -3053,9 +3827,9 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">4-atom selection in the correct order.  If no C&#8217;
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">4-atom selection in the correct order.  If no C&#8217;
 found in the previous residue (by resid) then this
-method returns <tt class="docutils literal"><span class="pre">None</span></tt>.</td>
+method returns <code class="docutils literal"><span class="pre">None</span></code>.</td>
 </tr>
 </tbody>
 </table>
@@ -3063,15 +3837,15 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.Residue.phi_selection">
-<tt class="descname">phi_selection</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Residue.phi_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Residue.phi_selection" title="Permalink to this definition">¶</a></dt>
+<code class="descname">phi_selection</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Residue.phi_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Residue.phi_selection" title="Permalink to this definition">¶</a></dt>
 <dd><p>AtomGroup corresponding to the phi protein backbone dihedral C&#8217;-N-CA-C.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">4-atom selection in the correct order.  If no C&#8217;
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">4-atom selection in the correct order.  If no C&#8217;
 found in the previous residue (by resid) then this
-method returns <tt class="docutils literal"><span class="pre">None</span></tt>.</td>
+method returns <code class="docutils literal"><span class="pre">None</span></code>.</td>
 </tr>
 </tbody>
 </table>
@@ -3079,15 +3853,15 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.Residue.psi_selection">
-<tt class="descname">psi_selection</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Residue.psi_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Residue.psi_selection" title="Permalink to this definition">¶</a></dt>
+<code class="descname">psi_selection</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Residue.psi_selection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Residue.psi_selection" title="Permalink to this definition">¶</a></dt>
 <dd><p>AtomGroup corresponding to the psi protein backbone dihedral N-CA-C-N&#8217;.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">4-atom selection in the correct order.  If no N&#8217;
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">4-atom selection in the correct order.  If no N&#8217;
 found in the following residue (by resid) then this
-method returns <tt class="docutils literal"><span class="pre">None</span></tt>.</td>
+method returns <code class="docutils literal"><span class="pre">None</span></code>.</td>
 </tr>
 </tbody>
 </table>
@@ -3097,13 +3871,13 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="class">
 <dt id="MDAnalysis.core.AtomGroup.ResidueGroup">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">ResidueGroup</tt><big>(</big><em>residues</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#ResidueGroup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">ResidueGroup</code><span class="sig-paren">(</span><em>residues</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#ResidueGroup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="Permalink to this definition">¶</a></dt>
 <dd><p>A group of residues.</p>
 <dl class="docutils">
 <dt>Pythonic access to atoms:</dt>
 <dd><ul class="first last">
 <li><p class="first">Using a atom name as attribute returns a list of all atoms (a
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>) of the same name. Example:</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>) of the same name. Example:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">MDAnalysis.tests.datafiles</span> <span class="kn">import</span> <span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">u</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="k">print</span><span class="p">(</span><span class="n">u</span><span class="o">.</span><span class="n">s4AKE</span><span class="o">.</span><span class="n">MET</span><span class="o">.</span><span class="n">CA</span><span class="p">)</span>  <span class="c"># C-alpha of all Met</span>
@@ -3118,35 +3892,130 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Data :</th><td class="field-body"><tt class="xref py py-attr docutils literal"><span class="pre">ResidueGroup._residues</span></tt></td>
+<tr class="field-odd field"><th class="field-name">Data:</th><td class="field-body"><code class="xref py py-attr docutils literal"><span class="pre">ResidueGroup._residues</span></code></td>
 </tr>
 </tbody>
 </table>
-<p>Initialize the ResidueGroup with a list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> instances.</p>
+<p>Initialize the ResidueGroup with a list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> instances.</p>
+<dl class="attribute">
+<dt id="MDAnalysis.core.AtomGroup.ResidueGroup.resids">
+<code class="descname">resids</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.resids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an array of residue numbers.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property and returns array of length <cite>len(self)</cite></p>
+</div>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="MDAnalysis.core.AtomGroup.ResidueGroup.resnames">
+<code class="descname">resnames</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.resnames" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an array of residue names.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property and returns array of length <cite>len(self)</cite></p>
+</div>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="MDAnalysis.core.AtomGroup.ResidueGroup.resnums">
+<code class="descname">resnums</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.resnums" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an array of canonical residue numbers.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property and returns array of length <cite>len(self)</cite></p>
+</div>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="MDAnalysis.core.AtomGroup.ResidueGroup.segids">
+<code class="descname">segids</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.segids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an array of segment names.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">uses the segment of the first atom in each residue for the
+segment name returned</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property and returns array of length <cite>len(self)</cite></p>
+</div>
+</dd></dl>
+
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.ResidueGroup.set">
-<tt class="descname">set</tt><big>(</big><em>name</em>, <em>value</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set attribute <em>name</em> to <em>value</em> for all residues in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a>.</p>
+<code class="descname">set</code><span class="sig-paren">(</span><em>name</em>, <em>value</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set attribute <em>name</em> to <em>value</em> for all residues in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>.</p>
 <p>If <em>value</em> is a sequence of the same length as the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a> (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="MDAnalysis.core.AtomGroup.AtomGroup.residues"><tt class="xref py py-attr docutils literal"><span class="pre">AtomGroup.residues</span></tt></a>) then each
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a>&#8216;s property <em>name</em> is set to the corresponding
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a> (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="MDAnalysis.core.AtomGroup.AtomGroup.residues"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.residues</span></code></a>) then each
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a>&#8216;s property <em>name</em> is set to the corresponding
 value. If <em>value</em> is neither of length 1 (or a scalar) nor of the
-length of the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set residues to distinct values by providing a sequence or iterable.</p>
+length of the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set residues to distinct values by providing a sequence or iterable.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.ResidueGroup.set_resid">
-<tt class="descname">set_resid</tt><big>(</big><em>resid</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#ResidueGroup.set_resid"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resid" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the resid to integer <em>resid</em> for <strong>all residues</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a>.</p>
-<p>If <em>resid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a>
-then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="MDAnalysis.core.AtomGroup.Atom.resid"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.resid</span></tt></a> is set to the corresponding value together
-with the <tt class="xref py py-attr docutils literal"><span class="pre">Residue.id</span></tt> of the residue the atom belongs to. If
+<code class="descname">set_resid</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resid" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_resid</cite> is deprecated, use <cite>set_resids</cite> instead!</p>
+<dl class="docutils">
+<dt>Set the resids to integer <em>resid</em> for <strong>all residues</strong> in the</dt>
+<dd><p class="first"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>.</p>
+<p>If <em>resid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="MDAnalysis.core.AtomGroup.Atom.resid"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resid</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.id</span></code> of the residue the atom belongs to. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p>Changing resids can change the topology.</p>
+<p class="last">Assigning the same <em>resid</em> to multiple residues will <strong>merge</strong> these
+residues. The new residue name will be the name of the first old
+residue in the merged residue.</p>
+</div>
+<div class="admonition warning">
+<p class="first admonition-title">Warning</p>
+<p class="last">The values of <em>this</em> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a> are not being
+changed. You <strong>must create a new</strong> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a> <strong>from the</strong>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> &#8212; only <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances are changed,
+everything else is derived from these atoms.</p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="last versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.ResidueGroup.set_resids">
+<code class="descname">set_resids</code><span class="sig-paren">(</span><em>resid</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#ResidueGroup.set_resids"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the resids to integer <em>resid</em> for <strong>all residues</strong> in the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>.</p>
+<p>If <em>resid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resid" title="MDAnalysis.core.AtomGroup.Atom.resid"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resid</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.id</span></code> of the residue the atom belongs to. If
 <em>value</em> is neither of length 1 (or a scalar) nor of the length of the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p>Changing resids can change the topology.</p>
@@ -3156,68 +4025,148 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </div>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
-<p class="last">The values of <em>this</em> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a> are not being
-changed. You <strong>must create a new</strong> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a> <strong>from the</strong>
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> &#8212; only <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances are changed,
+<p class="last">The values of <em>this</em> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a> are not being
+changed. You <strong>must create a new</strong> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a> <strong>from the</strong>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> &#8212; only <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances are changed,
 everything else is derived from these atoms.</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.ResidueGroup.set_resname">
-<tt class="descname">set_resname</tt><big>(</big><em>resname</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#ResidueGroup.set_resname"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resname" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the resname to string <em>resname</em> for <strong>all residues</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a>.</p>
-<p>If <em>resname</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a>
-then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resname" title="MDAnalysis.core.AtomGroup.Atom.resname"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.resname</span></tt></a> is set to the corresponding value together
-with the <tt class="xref py py-attr docutils literal"><span class="pre">Residue.name</span></tt> of the residue the atom belongs to. If
+<code class="descname">set_resname</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resname" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_resname</cite> is deprecated, use <cite>set_resnames</cite> instead!</p>
+<dl class="docutils">
+<dt>Set the resnames to string <em>resname</em> for <strong>all residues</strong> in the</dt>
+<dd><p class="first"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>.</p>
+<p>If <em>resname</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resname" title="MDAnalysis.core.AtomGroup.Atom.resname"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resname</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.name</span></code> of the residue the atom belongs to. If
 <em>value</em> is neither of length 1 (or a scalar) nor of the length of the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="last versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.ResidueGroup.set_resnames">
+<code class="descname">set_resnames</code><span class="sig-paren">(</span><em>resname</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#ResidueGroup.set_resnames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resnames" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the resnames to string <em>resname</em> for <strong>all residues</strong> in the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>.</p>
+<p>If <em>resname</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resname" title="MDAnalysis.core.AtomGroup.Atom.resname"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resname</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.name</span></code> of the residue the atom belongs to. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.ResidueGroup.set_resnum">
-<tt class="descname">set_resnum</tt><big>(</big><em>resnum</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#ResidueGroup.set_resnum"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resnum" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the resnum to <em>resnum</em> for <strong>all residues</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a>.</p>
-<p>If <em>resnum</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a>
-then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resnum" title="MDAnalysis.core.AtomGroup.Atom.resnum"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.resnum</span></tt></a> is set to the corresponding value together
-with the <tt class="xref py py-attr docutils literal"><span class="pre">Residue.resnum</span></tt> of the residue the atom belongs to. If
+<code class="descname">set_resnum</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resnum" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_resnum</cite> is deprecated, use <cite>set_resnums</cite> instead!</p>
+<p>Set the resnums to <em>resnum</em> for <strong>all residues</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>.</p>
+<blockquote>
+<div><p>If <em>resnum</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resnum" title="MDAnalysis.core.AtomGroup.Atom.resnum"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resnum</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.resnum</span></code> of the residue the atom belongs to. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">Changing <em>resnum</em> will not affect the topology: you can have
+multiple residues with the same <em>resnum</em>.</p>
+</div>
+<div class="admonition seealso">
+<p class="first admonition-title">See also</p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resid" title="MDAnalysis.core.AtomGroup.ResidueGroup.set_resid"><code class="xref py py-meth docutils literal"><span class="pre">set_resid()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.ResidueGroup.set_resnums">
+<code class="descname">set_resnums</code><span class="sig-paren">(</span><em>resnum</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#ResidueGroup.set_resnums"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resnums" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the resnums to <em>resnum</em> for <strong>all residues</strong> in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>.</p>
+<p>If <em>resnum</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.resnum" title="MDAnalysis.core.AtomGroup.Atom.resnum"><code class="xref py py-attr docutils literal"><span class="pre">Atom.resnum</span></code></a> is set to the corresponding value together
+with the <code class="xref py py-attr docutils literal"><span class="pre">Residue.resnum</span></code> of the residue the atom belongs to. If
 <em>value</em> is neither of length 1 (or a scalar) nor of the length of the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">Changing <em>resnum</em> will not affect the topology: you can have
 multiple residues with the same <em>resnum</em>.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resid" title="MDAnalysis.core.AtomGroup.ResidueGroup.set_resid"><tt class="xref py py-meth docutils literal"><span class="pre">set_resid()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup.set_resid" title="MDAnalysis.core.AtomGroup.ResidueGroup.set_resid"><code class="xref py py-meth docutils literal"><span class="pre">set_resid()</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Also changes the residues.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.AtomGroup.Segment">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">Segment</tt><big>(</big><em>name</em>, <em>residues</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Segment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Segment" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">Segment</code><span class="sig-paren">(</span><em>name</em>, <em>residues</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Segment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Segment" title="Permalink to this definition">¶</a></dt>
 <dd><p>A group of residues corresponding to one segment of the topology.</p>
 <p>Pythonic access to residues:</p>
 <blockquote>
 <div><ul>
-<li><p class="first">The attribute rN returns the N-th residue <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> of the
+<li><p class="first">The attribute rN returns the N-th residue <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> of the
 segment (numbering starts at N=1). Example:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">MDAnalysis.tests.datafiles</span> <span class="kn">import</span> <span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">u</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span><span class="p">)</span>
@@ -3227,7 +4176,7 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 </div>
 </li>
 <li><p class="first">Using a residue name as attribute returns a list of all residues (a
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></a>) of the same name. Example:</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.ResidueGroup" title="MDAnalysis.core.AtomGroup.ResidueGroup"><code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></a>) of the same name. Example:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">MDAnalysis.tests.datafiles</span> <span class="kn">import</span> <span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">u</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span><span class="n">DCD</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="k">print</span><span class="p">(</span><span class="n">u</span><span class="o">.</span><span class="n">s4AKE</span><span class="o">.</span><span class="n">CYS</span><span class="p">)</span>
@@ -3244,23 +4193,23 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Data :</th><td class="field-body"><tt class="xref py py-attr docutils literal"><span class="pre">Segment.name</span></tt> is the segid from the topology or the
+<tr class="field-odd field"><th class="field-name">Data:</th><td class="field-body"><code class="xref py py-attr docutils literal"><span class="pre">Segment.name</span></code> is the segid from the topology or the
 chain identifier when loaded from a PDB</td>
 </tr>
 </tbody>
 </table>
-<p>Initialize a Segment with segid <em>name</em> from a list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> instances.</p>
+<p>Initialize a Segment with segid <em>name</em> from a list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> instances.</p>
 <dl class="attribute">
 <dt id="MDAnalysis.core.AtomGroup.Segment.id">
-<tt class="descname">id</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#Segment.id"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Segment.id" title="Permalink to this definition">¶</a></dt>
-<dd><p>Segment id (alias for <tt class="xref py py-attr docutils literal"><span class="pre">Segment.name</span></tt>)</p>
+<code class="descname">id</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.Segment.id" title="Permalink to this definition">¶</a></dt>
+<dd><p>Segment id (alias for <code class="xref py py-attr docutils literal"><span class="pre">Segment.name</span></code>)</p>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.AtomGroup.SegmentGroup">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">SegmentGroup</tt><big>(</big><em>segments</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#SegmentGroup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">SegmentGroup</code><span class="sig-paren">(</span><em>segments</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#SegmentGroup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="Permalink to this definition">¶</a></dt>
 <dd><p>A group of segments.</p>
 <dl class="docutils">
 <dt>Pythonic access to segments:</dt>
@@ -3285,77 +4234,112 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Data :</th><td class="field-body"><tt class="xref py py-attr docutils literal"><span class="pre">SegmentGroup._segments</span></tt></td>
+<tr class="field-odd field"><th class="field-name">Data:</th><td class="field-body"><code class="xref py py-attr docutils literal"><span class="pre">SegmentGroup._segments</span></code></td>
 </tr>
 </tbody>
 </table>
-<p>Initialize the SegmentGroup with a list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a> instances.</p>
+<p>Initialize the SegmentGroup with a list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></a> instances.</p>
+<dl class="attribute">
+<dt id="MDAnalysis.core.AtomGroup.SegmentGroup.segids">
+<code class="descname">segids</code><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SegmentGroup.segids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an array of segment names.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Returns a <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Now a property and returns array of length <cite>len(self)</cite></p>
+</div>
+</dd></dl>
+
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.SegmentGroup.set">
-<tt class="descname">set</tt><big>(</big><em>name</em>, <em>value</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SegmentGroup.set" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set attribute <em>name</em> to <em>value</em> for all <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a> in this <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>.</p>
+<code class="descname">set</code><span class="sig-paren">(</span><em>name</em>, <em>value</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SegmentGroup.set" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set attribute <em>name</em> to <em>value</em> for all <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></a> in this <a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
 <p>If <em>value</em> is a sequence of the same length as the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></a> (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="MDAnalysis.core.AtomGroup.AtomGroup.residues"><tt class="xref py py-attr docutils literal"><span class="pre">AtomGroup.residues</span></tt></a>) then each
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a>&#8216;s property <em>name</em> is set to the corresponding
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code></a> (<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="MDAnalysis.core.AtomGroup.AtomGroup.residues"><code class="xref py py-attr docutils literal"><span class="pre">AtomGroup.residues</span></code></a>) then each
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></a>&#8216;s property <em>name</em> is set to the corresponding
 value. If <em>value</em> is neither of length 1 (or a scalar) nor of the
-length of the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+length of the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.AtomGroup.SegmentGroup.set_segid">
-<tt class="descname">set_segid</tt><big>(</big><em>segid</em>, <em>buildsegments=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#SegmentGroup.set_segid"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SegmentGroup.set_segid" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the segid to <em>segid</em> for all atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></a>.</p>
-<p>If <em>segid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></a>
-then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><tt class="xref py py-attr docutils literal"><span class="pre">Atom.segid</span></tt></a> is set to the corresponding value together
-with the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment.id" title="MDAnalysis.core.AtomGroup.Segment.id"><tt class="xref py py-attr docutils literal"><span class="pre">Segment.id</span></tt></a> of the segment the atom belongs to. If
+<code class="descname">set_segid</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SegmentGroup.set_segid" title="Permalink to this definition">¶</a></dt>
+<dd><p><cite>set_segid</cite> is deprecated, use <cite>set_segids</cite> instead!</p>
+<p>Set the segids to <em>segid</em> for all atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code></a>.</p>
+<blockquote>
+<div><p>If <em>segid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><code class="xref py py-attr docutils literal"><span class="pre">Atom.segid</span></code></a> is set to the corresponding value together
+with the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment.id" title="MDAnalysis.core.AtomGroup.Segment.id"><code class="xref py py-attr docutils literal"><span class="pre">Segment.id</span></code></a> of the segment the atom belongs to. If
 <em>value</em> is neither of length 1 (or a scalar) nor of the length of the
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> then a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> is raised.</p>
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup.set_segid" title="MDAnalysis.core.AtomGroup.SegmentGroup.set_segid"><tt class="xref py py-meth docutils literal"><span class="pre">set_segid()</span></tt></a> can change the topology.</p>
-<p class="last">With the default <em>buildsegments</em> = <tt class="docutils literal"><span class="pre">True</span></tt> it can be used to join
-segments or to break groups into multiple disjoint segments. Note
-that each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> can only belong to a single
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a>.</p>
-</div>
-<p>For performance reasons, <em>buildsegments</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt>. Then
-one needs to run <tt class="xref py py-meth docutils literal"><span class="pre">Universe._build_segments()</span></tt> manually later in
-order to update the list of <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a> instances and regenerate
-the segid instant selectors.</p>
-<div class="admonition warning">
-<p class="first admonition-title">Warning</p>
-<p class="last">The values of <em>this</em> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></a> are not being changed
-(i.e. if you assign multiple segids this instance will not be broken
-in multiple segments, rather you will have one <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></a>
-that groups multiple segments together). You <strong>must create a new</strong>
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></a> <strong>from the</strong> <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> &#8212; only
-<a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances are changed, everything else is derived from
-these atoms.</p>
+<p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup.set_segid" title="MDAnalysis.core.AtomGroup.SegmentGroup.set_segid"><code class="xref py py-meth docutils literal"><span class="pre">set_segid()</span></code></a> can change the topology.</p>
+<p class="last">This can be used to join segments or to break groups into multiple
+disjoint segments. Note that each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> can only belong to a
+single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></a>.</p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
+</div>
+</div></blockquote>
+</dd></dl>
+
+<dl class="method">
+<dt id="MDAnalysis.core.AtomGroup.SegmentGroup.set_segids">
+<code class="descname">set_segids</code><span class="sig-paren">(</span><em>segid</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#SegmentGroup.set_segids"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SegmentGroup.set_segids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the segids to <em>segid</em> for all atoms in the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code></a>.</p>
+<p>If <em>segid</em> is a sequence of the same length as the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup" title="MDAnalysis.core.AtomGroup.SegmentGroup"><code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code></a>
+then each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom.segid" title="MDAnalysis.core.AtomGroup.Atom.segid"><code class="xref py py-attr docutils literal"><span class="pre">Atom.segid</span></code></a> is set to the corresponding value together
+with the <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment.id" title="MDAnalysis.core.AtomGroup.Segment.id"><code class="xref py py-attr docutils literal"><span class="pre">Segment.id</span></code></a> of the segment the atom belongs to. If
+<em>value</em> is neither of length 1 (or a scalar) nor of the length of the
+<a class="reference internal" href="#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> then a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> is raised.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p><a class="reference internal" href="#MDAnalysis.core.AtomGroup.SegmentGroup.set_segid" title="MDAnalysis.core.AtomGroup.SegmentGroup.set_segid"><code class="xref py py-meth docutils literal"><span class="pre">set_segid()</span></code></a> can change the topology.</p>
+<p class="last">This can be used to join segments or to break groups into multiple
+disjoint segments. Note that each <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> can only belong to a
+single <a class="reference internal" href="#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></a>.</p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.4.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Made plural to make consistent with corresponding property</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.4.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Can set atoms and residues to distinct values by providing a sequence or iterable.</p>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="function">
-<dt id="MDAnalysis.core.AtomGroup.asUniverse">
-<tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">asUniverse</tt><big>(</big><em>*args</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#asUniverse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.asUniverse" title="Permalink to this definition">¶</a></dt>
+<dt id="MDAnalysis.core.AtomGroup.as_Universe">
+<code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">as_Universe</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/AtomGroup.html#as_Universe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.as_Universe" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return a universe from the input arguments.</p>
 <ol class="arabic">
 <li><p class="first">If the first argument is a universe, just return it:</p>
-<div class="highlight-python"><pre>as_universe(universe) --&gt; universe</pre>
+<div class="highlight-python"><div class="highlight"><pre>as_Universe(universe) --&gt; universe
+</pre></div>
 </div>
 </li>
 <li><p class="first">Otherwise try to build a universe from the first or the first
 and second argument:</p>
-<div class="highlight-python"><pre>asUniverse(PDB, **kwargs) --&gt; Universe(PDB, **kwargs)
-asUniverse(PSF, DCD, **kwargs) --&gt; Universe(PSF, DCD, **kwargs)
-asUniverse(*args, **kwargs) --&gt; Universe(*args, **kwargs)</pre>
+<div class="highlight-python"><div class="highlight"><pre>as_Universe(PDB, **kwargs) --&gt; Universe(PDB, **kwargs)
+as_Universe(PSF, DCD, **kwargs) --&gt; Universe(PSF, DCD, **kwargs)
+as_Universe(*args, **kwargs) --&gt; Universe(*args, **kwargs)
+</pre></div>
 </div>
 </li>
 </ol>
@@ -3363,7 +4347,7 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">an instance of <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">an instance of <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></td>
 </tr>
 </tbody>
 </table>
@@ -3371,19 +4355,19 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
 
 <dl class="exception">
 <dt id="MDAnalysis.core.AtomGroup.SelectionError">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">SelectionError</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SelectionError" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">SelectionError</code><a class="reference internal" href="../../_modules/MDAnalysis/exceptions.html#SelectionError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SelectionError" title="Permalink to this definition">¶</a></dt>
 <dd><p>Raised when a atom selection failed.</p>
 </dd></dl>
 
 <dl class="exception">
 <dt id="MDAnalysis.core.AtomGroup.SelectionWarning">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">SelectionWarning</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SelectionWarning" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">SelectionWarning</code><a class="reference internal" href="../../_modules/MDAnalysis/exceptions.html#SelectionWarning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.SelectionWarning" title="Permalink to this definition">¶</a></dt>
 <dd><p>Warning indicating a possible problem with a selection.</p>
 </dd></dl>
 
 <dl class="exception">
 <dt id="MDAnalysis.core.AtomGroup.NoDataError">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.core.AtomGroup.</tt><tt class="descname">NoDataError</tt><a class="headerlink" href="#MDAnalysis.core.AtomGroup.NoDataError" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.core.AtomGroup.</code><code class="descname">NoDataError</code><a class="reference internal" href="../../_modules/MDAnalysis/exceptions.html#NoDataError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.AtomGroup.NoDataError" title="Permalink to this definition">¶</a></dt>
 <dd><p>Raised when empty input is not allowed or required data are missing.</p>
 </dd></dl>
 
@@ -3396,7 +4380,7 @@ <h2>7.2.5. Classes and functions<a class="headerlink" href="#classes-and-functio
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -3411,11 +4395,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="init.html" title="7.1. Core functions of MDAnalysis"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../core_modules.html" >7. Core modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../core_modules.html" >7. Core modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -3425,7 +4409,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/Selection.html b/package/doc/html/documentation_pages/core/Selection.html
index 6a46c1e2532..92d9f781f7a 100644
--- a/package/doc/html/documentation_pages/core/Selection.html
+++ b/package/doc/html/documentation_pages/core/Selection.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>7.3. Atom selection Hierarchy — MDAnalysis.core.Selection &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>7.3. Atom selection Hierarchy — MDAnalysis.core.Selection &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="7. Core modules" href="../core_modules.html" />
     <link rel="next" title="7.4. Core Topology Objects — MDAnalysis.core.topologyobjects" href="topologyobjects.html" />
     <link rel="prev" title="7.2. Fundamental building blocks — MDAnalysis.core.AtomGroup" href="AtomGroup.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="AtomGroup.html" title="7.2. Fundamental building blocks — MDAnalysis.core.AtomGroup"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../core_modules.html" accesskey="U">7. Core modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../core_modules.html" accesskey="U">7. Core modules</a> &raquo;</li> 
       </ul>
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="AtomGroup.html"
-                        title="previous chapter">7.2. Fundamental building blocks &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></tt></a></p>
+                        title="previous chapter">7.2. Fundamental building blocks &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="topologyobjects.html"
-                        title="next chapter">7.4. Core Topology Objects &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.core.topologyobjects</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/core/Selection.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">7.4. Core Topology Objects &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.topologyobjects</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/core/Selection.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,22 +90,22 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.core.Selection"></span><div class="section" id="atom-selection-hierarchy-mdanalysis-core-selection">
-<h1>7.3. Atom selection Hierarchy &#8212; <a class="reference internal" href="#module-MDAnalysis.core.Selection" title="MDAnalysis.core.Selection"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.Selection</span></tt></a><a class="headerlink" href="#atom-selection-hierarchy-mdanalysis-core-selection" title="Permalink to this headline">¶</a></h1>
+<h1>7.3. Atom selection Hierarchy &#8212; <a class="reference internal" href="#module-MDAnalysis.core.Selection" title="MDAnalysis.core.Selection"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.Selection</span></code></a><a class="headerlink" href="#atom-selection-hierarchy-mdanalysis-core-selection" title="Permalink to this headline">¶</a></h1>
 <p>These objects are constructed and applied to the group</p>
 <p>Currently all atom arrays are handled internally as sets, but returned as AtomGroups</p>
 <dl class="class">
 <dt id="MDAnalysis.core.Selection.BackboneSelection">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Selection.</tt><tt class="descname">BackboneSelection</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#BackboneSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.BackboneSelection" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Selection.</code><code class="descname">BackboneSelection</code><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#BackboneSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.BackboneSelection" title="Permalink to this definition">¶</a></dt>
 <dd><p>A BackboneSelection contains all atoms with name &#8216;N&#8217;, &#8216;CA&#8217;, &#8216;C&#8217;, &#8216;O&#8217;.</p>
 <p>This excludes OT* on C-termini (which are included by, eg VMD&#8217;s backbone selection).</p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Selection.BaseSelection">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Selection.</tt><tt class="descname">BaseSelection</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#BaseSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.BaseSelection" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Selection.</code><code class="descname">BaseSelection</code><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#BaseSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.BaseSelection" title="Permalink to this definition">¶</a></dt>
 <dd><p>Selection of atoms in nucleobases.</p>
 <p>Recognized atom names (from CHARMM):</p>
 <blockquote>
@@ -115,21 +115,21 @@ <h1>7.3. Atom selection Hierarchy &#8212; <a class="reference internal" href="#m
 
 <dl class="class">
 <dt id="MDAnalysis.core.Selection.CASelection">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Selection.</tt><tt class="descname">CASelection</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#CASelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.CASelection" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Selection.</code><code class="descname">CASelection</code><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#CASelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.CASelection" title="Permalink to this definition">¶</a></dt>
 <dd><p>Select atoms named CA in protein residues (supposed to be the C-alphas)</p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Selection.NucleicBackboneSelection">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Selection.</tt><tt class="descname">NucleicBackboneSelection</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#NucleicBackboneSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.NucleicBackboneSelection" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Selection.</code><code class="descname">NucleicBackboneSelection</code><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#NucleicBackboneSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.NucleicBackboneSelection" title="Permalink to this definition">¶</a></dt>
 <dd><p>A NucleicBackboneSelection contains all atoms with name &#8220;P&#8221;, &#8220;C5&#8217;&#8221;, C3&#8217;&#8221;, &#8220;O3&#8217;&#8221;, &#8220;O5&#8217;&#8221;.</p>
 <p>These atoms are only recognized if they are in a residue matched
-by the <a class="reference internal" href="#MDAnalysis.core.Selection.NucleicSelection" title="MDAnalysis.core.Selection.NucleicSelection"><tt class="xref py py-class docutils literal"><span class="pre">NucleicSelection</span></tt></a>.</p>
+by the <a class="reference internal" href="#MDAnalysis.core.Selection.NucleicSelection" title="MDAnalysis.core.Selection.NucleicSelection"><code class="xref py py-class docutils literal"><span class="pre">NucleicSelection</span></code></a>.</p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Selection.NucleicSelection">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Selection.</tt><tt class="descname">NucleicSelection</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#NucleicSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.NucleicSelection" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Selection.</code><code class="descname">NucleicSelection</code><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#NucleicSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.NucleicSelection" title="Permalink to this definition">¶</a></dt>
 <dd><p>A nucleic selection consists of all atoms in nucleic acid residues with  recognized residue names.</p>
 <p>Recognized residue names:</p>
 <ul>
@@ -144,28 +144,29 @@ <h1>7.3. Atom selection Hierarchy &#8212; <a class="reference internal" href="#m
 <li><p class="first">recognized (CHARMM in Gromacs): &#8216;DA&#8217;, &#8216;DU&#8217;, &#8216;DC&#8217;, &#8216;DG&#8217;, &#8216;DT&#8217;</p>
 </li>
 </ul>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>additional Gromacs selections (see also <tt class="xref py py-class docutils literal"><span class="pre">NucleicXstalSelection</span></tt>)</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>additional Gromacs selections (see also <code class="xref py py-class docutils literal"><span class="pre">NucleicXstalSelection</span></code>)</p>
+</div>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Selection.NucleicSugarSelection">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Selection.</tt><tt class="descname">NucleicSugarSelection</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#NucleicSugarSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.NucleicSugarSelection" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Selection.</code><code class="descname">NucleicSugarSelection</code><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#NucleicSugarSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.NucleicSugarSelection" title="Permalink to this definition">¶</a></dt>
 <dd><p>A NucleicSugarSelection contains all atoms with name C1&#8217;, C2&#8217;, C3&#8217;, C4&#8217;, O2&#8217;, O4&#8217;, O3&#8217;.</p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Selection.PropertySelection">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Selection.</tt><tt class="descname">PropertySelection</tt><big>(</big><em>prop</em>, <em>operator</em>, <em>value</em>, <em>abs=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#PropertySelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.PropertySelection" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Selection.</code><code class="descname">PropertySelection</code><span class="sig-paren">(</span><em>prop</em>, <em>operator</em>, <em>value</em>, <em>abs=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#PropertySelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.PropertySelection" title="Permalink to this definition">¶</a></dt>
 <dd><p>Some of the possible properties:
 x, y, z, radius, mass,</p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Selection.ProteinSelection">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Selection.</tt><tt class="descname">ProteinSelection</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#ProteinSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.ProteinSelection" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Selection.</code><code class="descname">ProteinSelection</code><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#ProteinSelection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.ProteinSelection" title="Permalink to this definition">¶</a></dt>
 <dd><p>A protein selection consists of all residues with  recognized residue names.</p>
-<p>Recognized residue names in <a class="reference internal" href="#MDAnalysis.core.Selection.ProteinSelection.prot_res" title="MDAnalysis.core.Selection.ProteinSelection.prot_res"><tt class="xref py py-attr docutils literal"><span class="pre">ProteinSelection.prot_res</span></tt></a>.</p>
+<p>Recognized residue names in <a class="reference internal" href="#MDAnalysis.core.Selection.ProteinSelection.prot_res" title="MDAnalysis.core.Selection.ProteinSelection.prot_res"><code class="xref py py-attr docutils literal"><span class="pre">ProteinSelection.prot_res</span></code></a>.</p>
 <blockquote>
 <div><ul>
 <li><dl class="first docutils">
@@ -180,13 +181,13 @@ <h1>7.3. Atom selection Hierarchy &#8212; <a class="reference internal" href="#m
 </li>
 </ul>
 </div></blockquote>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../lib/util.html#MDAnalysis.lib.util.convert_aa_code" title="MDAnalysis.lib.util.convert_aa_code"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.util.convert_aa_code()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="../lib/util.html#MDAnalysis.lib.util.convert_aa_code" title="MDAnalysis.lib.util.convert_aa_code"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.util.convert_aa_code()</span></code></a></p>
 </div>
 <dl class="attribute">
 <dt id="MDAnalysis.core.Selection.ProteinSelection.prot_res">
-<tt class="descname">prot_res</tt><em class="property"> = {'GLH': None, 'ILE': None, 'ALAD': None, 'GLUH': None, 'GLN': None, 'HISH': None, 'ASN1': None, 'HYP': None, 'GLY': None, 'HIP': None, 'ARGN': None, 'MSE': None, 'CYS1': None, 'GLU': None, 'CYS2': None, 'CYS': None, 'HISE': None, 'ASP': None, 'SER': None, 'HSD': None, 'HSE': None, 'PRO': None, 'CYX': None, 'ASPH': None, 'ORN': None, 'HSP': None, 'HID': None, 'HIE': None, 'LYN': None, 'DAB': None, 'ASN': None, 'CYM': None, 'HISD': None, 'VAL': None, 'THR': None, 'HISB': None, 'HIS': None, 'HIS1': None, 'HIS2': None, 'TRP': None, 'HISA': None, 'ACE': None, 'ASH': None, 'CYSH': None, 'PGLU': None, 'LYS': None, 'PHE': None, 'ALA': None, 'QLN': None, 'MET': None, 'LYSH': None, 'NME': None, 'LEU': None, 'ARG': None, 'TYR': None}</em><a class="headerlink" href="#MDAnalysis.core.Selection.ProteinSelection.prot_res" title="Permalink to this definition">¶</a></dt>
+<code class="descname">prot_res</code><em class="property"> = {'GLH': None, 'ILE': None, 'ALAD': None, 'GLUH': None, 'GLN': None, 'HISH': None, 'ASN1': None, 'HYP': None, 'GLY': None, 'HIP': None, 'ARGN': None, 'MSE': None, 'CYS1': None, 'GLU': None, 'CYS2': None, 'CYS': None, 'HISE': None, 'ASP': None, 'SER': None, 'HSD': None, 'HSE': None, 'PRO': None, 'CYX': None, 'ASPH': None, 'ORN': None, 'HSP': None, 'HID': None, 'HIE': None, 'LYN': None, 'DAB': None, 'ASN': None, 'CYM': None, 'HISD': None, 'VAL': None, 'THR': None, 'HISB': None, 'HIS': None, 'HIS1': None, 'HIS2': None, 'TRP': None, 'HISA': None, 'ACE': None, 'ASH': None, 'CYSH': None, 'PGLU': None, 'LYS': None, 'PHE': None, 'ALA': None, 'QLN': None, 'MET': None, 'LYSH': None, 'NME': None, 'LEU': None, 'ARG': None, 'TYR': None}</em><a class="headerlink" href="#MDAnalysis.core.Selection.ProteinSelection.prot_res" title="Permalink to this definition">¶</a></dt>
 <dd><p>Dictionary of recognized residue names (3- or 4-letter).</p>
 </dd></dl>
 
@@ -194,22 +195,23 @@ <h1>7.3. Atom selection Hierarchy &#8212; <a class="reference internal" href="#m
 
 <dl class="class">
 <dt id="MDAnalysis.core.Selection.SelectionParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Selection.</tt><tt class="descname">SelectionParser</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#SelectionParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.SelectionParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Selection.</code><code class="descname">SelectionParser</code><a class="reference internal" href="../../_modules/MDAnalysis/core/Selection.html#SelectionParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Selection.SelectionParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>A small parser for selection expressions.  Demonstration of
 recursive descent parsing using Precedence climbing (see
 <a class="reference external" href="http://www.engr.mun.ca/~theo/Misc/exp_parsing.htm">http://www.engr.mun.ca/~theo/Misc/exp_parsing.htm</a>).  Transforms
 expressions into nested Selection tree.</p>
 <p>For reference, the grammar that we parse is</p>
-<div class="highlight-python"><pre>E(xpression)--&gt; Exp(0)
+<div class="highlight-python"><div class="highlight"><pre>E(xpression)--&gt; Exp(0)
 Exp(p) --&gt;      P {B Exp(q)}
-P --&gt;           U Exp(q) | "(" E ")" | v
-B(inary) --&gt;    "and" | "or"
-U(nary) --&gt;     "not"
+P --&gt;           U Exp(q) | &quot;(&quot; E &quot;)&quot; | v
+B(inary) --&gt;    &quot;and&quot; | &quot;or&quot;
+U(nary) --&gt;     &quot;not&quot;
 T(erms) --&gt;     segid [value]
                 | resname [value]
                 | resid [value]
                 | name [value]
-                | type [value]</pre>
+                | type [value]
+</pre></div>
 </div>
 </dd></dl>
 
@@ -221,7 +223,7 @@ <h1>7.3. Atom selection Hierarchy &#8212; <a class="reference internal" href="#m
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -236,11 +238,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="AtomGroup.html" title="7.2. Fundamental building blocks — MDAnalysis.core.AtomGroup"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../core_modules.html" >7. Core modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../core_modules.html" >7. Core modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -250,7 +252,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/Timeseries.html b/package/doc/html/documentation_pages/core/Timeseries.html
index f275f2451d4..53695966c79 100644
--- a/package/doc/html/documentation_pages/core/Timeseries.html
+++ b/package/doc/html/documentation_pages/core/Timeseries.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>7.5. Compute observable timeseries from trajectories — MDAnalysis.core.Timeseries &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>7.5. Compute observable timeseries from trajectories — MDAnalysis.core.Timeseries &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="7. Core modules" href="../core_modules.html" />
     <link rel="next" title="8. Visualization modules" href="../visualization_modules.html" />
     <link rel="prev" title="7.4. Core Topology Objects — MDAnalysis.core.topologyobjects" href="topologyobjects.html" /> 
   </head>
-  <body>
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="topologyobjects.html" title="7.4. Core Topology Objects — MDAnalysis.core.topologyobjects"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../core_modules.html" accesskey="U">7. Core modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../core_modules.html" accesskey="U">7. Core modules</a> &raquo;</li> 
       </ul>
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">7.5. Compute observable timeseries from trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.core.Timeseries</span></tt></a><ul>
+<li><a class="reference internal" href="#">7.5. Compute observable timeseries from trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.Timeseries</span></code></a><ul>
 <li><a class="reference internal" href="#basic-classes">7.5.1. Basic classes</a></li>
 <li><a class="reference internal" href="#timeseries-of-observables">7.5.2. Timeseries of observables</a></li>
 </ul>
@@ -71,16 +69,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="topologyobjects.html"
-                        title="previous chapter">7.4. Core Topology Objects &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.core.topologyobjects</span></tt></a></p>
+                        title="previous chapter">7.4. Core Topology Objects &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.topologyobjects</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="../visualization_modules.html"
                         title="next chapter">8. Visualization modules</a></p>
-  <h3>This Page</h3>
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-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/core/Timeseries.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -99,26 +99,26 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.core.Timeseries"></span><div class="section" id="compute-observable-timeseries-from-trajectories-mdanalysis-core-timeseries">
-<h1>7.5. Compute observable timeseries from trajectories &#8212; <a class="reference internal" href="#module-MDAnalysis.core.Timeseries" title="MDAnalysis.core.Timeseries"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.Timeseries</span></tt></a><a class="headerlink" href="#compute-observable-timeseries-from-trajectories-mdanalysis-core-timeseries" title="Permalink to this headline">¶</a></h1>
-<p>The collection of timeseries (such as <a class="reference internal" href="#MDAnalysis.core.Timeseries.Atom" title="MDAnalysis.core.Timeseries.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>, <a class="reference internal" href="#MDAnalysis.core.Timeseries.Bond" title="MDAnalysis.core.Timeseries.Bond"><tt class="xref py py-class docutils literal"><span class="pre">Bond</span></tt></a>,
-<a class="reference internal" href="#MDAnalysis.core.Timeseries.Dihedral" title="MDAnalysis.core.Timeseries.Dihedral"><tt class="xref py py-class docutils literal"><span class="pre">Dihedral</span></tt></a>...)  can be computed from a trajectory in one go, foregoing
+<h1>7.5. Compute observable timeseries from trajectories &#8212; <a class="reference internal" href="#module-MDAnalysis.core.Timeseries" title="MDAnalysis.core.Timeseries"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.Timeseries</span></code></a><a class="headerlink" href="#compute-observable-timeseries-from-trajectories-mdanalysis-core-timeseries" title="Permalink to this headline">¶</a></h1>
+<p>The collection of timeseries (such as <a class="reference internal" href="#MDAnalysis.core.Timeseries.Atom" title="MDAnalysis.core.Timeseries.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>, <a class="reference internal" href="#MDAnalysis.core.Timeseries.Bond" title="MDAnalysis.core.Timeseries.Bond"><code class="xref py py-class docutils literal"><span class="pre">Bond</span></code></a>,
+<a class="reference internal" href="#MDAnalysis.core.Timeseries.Dihedral" title="MDAnalysis.core.Timeseries.Dihedral"><code class="xref py py-class docutils literal"><span class="pre">Dihedral</span></code></a>...)  can be computed from a trajectory in one go, foregoing
 the need to iterate through the trajectory frame by frame in python. Inspired
 by CHARMM&#8217;s correl command.</p>
 <p>The disadvantage is that the timeseries &#8216;plugins&#8217; must be implemented
-in C-code. Hence not all trajectory readers (see <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates</span></tt>)
+in C-code. Hence not all trajectory readers (see <code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates</span></code>)
 support them.</p>
 <div class="section" id="basic-classes">
 <h2>7.5.1. Basic classes<a class="headerlink" href="#basic-classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.core.Timeseries.Timeseries">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Timeseries.</tt><tt class="descname">Timeseries</tt><big>(</big><em>code</em>, <em>atoms</em>, <em>dsize</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Timeseries"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Timeseries" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Timeseries.</code><code class="descname">Timeseries</code><span class="sig-paren">(</span><em>code</em>, <em>atoms</em>, <em>dsize</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Timeseries"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Timeseries" title="Permalink to this definition">¶</a></dt>
 <dd><p>Base timeseries class - define subclasses for specific timeseries computations</p>
 <dl class="attribute">
 <dt id="MDAnalysis.core.Timeseries.Timeseries.shape">
-<tt class="descname">shape</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Timeseries.shape"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Timeseries.shape" title="Permalink to this definition">¶</a></dt>
+<code class="descname">shape</code><a class="headerlink" href="#MDAnalysis.core.Timeseries.Timeseries.shape" title="Permalink to this definition">¶</a></dt>
 <dd><p>shape tuple of the underlying numpy array</p>
 </dd></dl>
 
@@ -126,7 +126,7 @@ <h2>7.5.1. Basic classes<a class="headerlink" href="#basic-classes" title="Perma
 
 <dl class="class">
 <dt id="MDAnalysis.core.Timeseries.TimeseriesCollection">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Timeseries.</tt><tt class="descname">TimeseriesCollection</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#TimeseriesCollection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.TimeseriesCollection" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Timeseries.</code><code class="descname">TimeseriesCollection</code><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#TimeseriesCollection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.TimeseriesCollection" title="Permalink to this definition">¶</a></dt>
 <dd><p>A collection of timeseries objects.</p>
 <p>The collection of timeseries (such as Atom, Bond, Dihedral...)  can be
 computed from a trajectory in one go, foregoing the need to iterate through
@@ -134,32 +134,33 @@ <h2>7.5.1. Basic classes<a class="headerlink" href="#basic-classes" title="Perma
 command.</p>
 <p>The disadvantage is that the timeseries &#8216;plugins&#8217; must be implemented in
 C-code.</p>
-<div class="highlight-python"><pre>collection = TimeseriesCollection()
+<div class="highlight-python"><div class="highlight"><pre>collection = TimeseriesCollection()
 collection.addTimeseries(Timeseries.Atom(...)) - add a new Timeseries object
 collection.compute(...)                        - compute the collection of timeseries from the trajectory
 collection.clear()                             - clear the collection
-collection[i]                                  - access the i'th timeseries
-len(collection)                                - return the number of Timeseries added to the collection</pre>
+collection[i]                                  - access the i&#39;th timeseries
+len(collection)                                - return the number of Timeseries added to the collection
+</pre></div>
 </div>
 <dl class="method">
 <dt id="MDAnalysis.core.Timeseries.TimeseriesCollection.addTimeseries">
-<tt class="descname">addTimeseries</tt><big>(</big><em>ts</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#TimeseriesCollection.addTimeseries"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.TimeseriesCollection.addTimeseries" title="Permalink to this definition">¶</a></dt>
+<code class="descname">addTimeseries</code><span class="sig-paren">(</span><em>ts</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#TimeseriesCollection.addTimeseries"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.TimeseriesCollection.addTimeseries" title="Permalink to this definition">¶</a></dt>
 <dd><p>add a Timeseries object to the collection</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.Timeseries.TimeseriesCollection.clear">
-<tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#TimeseriesCollection.clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.TimeseriesCollection.clear" title="Permalink to this definition">¶</a></dt>
+<code class="descname">clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#TimeseriesCollection.clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.TimeseriesCollection.clear" title="Permalink to this definition">¶</a></dt>
 <dd><p>clear the timeseries collection</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.Timeseries.TimeseriesCollection.compute">
-<tt class="descname">compute</tt><big>(</big><em>trj</em>, <em>start=0</em>, <em>stop=-1</em>, <em>skip=1</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#TimeseriesCollection.compute"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.TimeseriesCollection.compute" title="Permalink to this definition">¶</a></dt>
+<code class="descname">compute</code><span class="sig-paren">(</span><em>trj</em>, <em>start=0</em>, <em>stop=-1</em>, <em>skip=1</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#TimeseriesCollection.compute"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.TimeseriesCollection.compute" title="Permalink to this definition">¶</a></dt>
 <dd><p>Iterate through the trajectory <em>trj</em> and compute the time series.</p>
 <dl class="docutils">
 <dt><em>trj</em></dt>
-<dd>dcd trajectory object (i.e. <tt class="xref py py-attr docutils literal"><span class="pre">Universe.trajectory</span></tt>)</dd>
+<dd>dcd trajectory object (i.e. <code class="xref py py-attr docutils literal"><span class="pre">Universe.trajectory</span></code>)</dd>
 <dt><em>start, stop, skip</em></dt>
 <dd>Frames to calculate parts of the trajectory. It is important to
 note that <em>start</em> and <em>stop</em> are inclusive</dd>
@@ -173,7 +174,7 @@ <h2>7.5.1. Basic classes<a class="headerlink" href="#basic-classes" title="Perma
 <h2>7.5.2. Timeseries of observables<a class="headerlink" href="#timeseries-of-observables" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.core.Timeseries.Atom">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Timeseries.</tt><tt class="descname">Atom</tt><big>(</big><em>code</em>, <em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Atom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Atom" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Timeseries.</code><code class="descname">Atom</code><span class="sig-paren">(</span><em>code</em>, <em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Atom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Atom" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a timeseries that returns coordinate data for an atom or group of atoms</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">t</span> <span class="o">=</span> <span class="n">Atom</span><span class="p">(</span><span class="n">code</span><span class="p">,</span> <span class="n">atoms</span><span class="p">)</span>
 </pre></div>
@@ -183,84 +184,84 @@ <h2>7.5.2. Timeseries of observables<a class="headerlink" href="#timeseries-of-o
 <dd>is one of &#8216;x&#8217;, &#8216;y&#8217;, &#8216;z&#8217;, or &#8216;v&#8217; (&#8216;vector&#8217;, which returns all three
 dimensions)</dd>
 <dt><em>atoms</em></dt>
-<dd>can be a single <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> object,
-a list of <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> objects, or an
-<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></dd>
+<dd>can be a single <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> object,
+a list of <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> objects, or an
+<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a></dd>
 </dl>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Timeseries.Bond">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Timeseries.</tt><tt class="descname">Bond</tt><big>(</big><em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Bond"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Bond" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Timeseries.</code><code class="descname">Bond</code><span class="sig-paren">(</span><em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Bond"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Bond" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a timeseries that returns a timeseries for a bond</p>
 <blockquote>
 <div>t = Bond(atoms)</div></blockquote>
-<p><em>atoms</em> must contain 2 <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances, either as a list or an
-<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></p>
+<p><em>atoms</em> must contain 2 <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances, either as a list or an
+<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a></p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Timeseries.Angle">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Timeseries.</tt><tt class="descname">Angle</tt><big>(</big><em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Angle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Angle" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Timeseries.</code><code class="descname">Angle</code><span class="sig-paren">(</span><em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Angle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Angle" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a timeseries that returns a timeseries for an angle</p>
 <blockquote>
 <div>t = Angle(atoms)</div></blockquote>
-<p>atoms must contain 3 <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances, either as a list or an
-<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></p>
+<p>atoms must contain 3 <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances, either as a list or an
+<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a></p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Timeseries.Dihedral">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Timeseries.</tt><tt class="descname">Dihedral</tt><big>(</big><em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Dihedral"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Dihedral" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Timeseries.</code><code class="descname">Dihedral</code><span class="sig-paren">(</span><em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Dihedral"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Dihedral" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a timeseries that returns a timeseries for a dihedral angle</p>
 <blockquote>
 <div>t = Dihedral(atoms)</div></blockquote>
-<p>atoms must contain 4 <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> objects, either as a list or an
-<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></p>
+<p>atoms must contain 4 <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> objects, either as a list or an
+<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a></p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Timeseries.Distance">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Timeseries.</tt><tt class="descname">Distance</tt><big>(</big><em>code</em>, <em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Distance"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Distance" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Timeseries.</code><code class="descname">Distance</code><span class="sig-paren">(</span><em>code</em>, <em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#Distance"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.Distance" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a timeseries that returns distances between 2 atoms</p>
 <blockquote>
 <div>t = Distance(code, atoms)</div></blockquote>
 <p>code is one of &#8216;d&#8217; (distance vector), or &#8216;r&#8217; (scalar distance)
-atoms must contain 2 <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> objects, either as a list or an
-<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></p>
+atoms must contain 2 <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> objects, either as a list or an
+<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a></p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Timeseries.CenterOfGeometry">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Timeseries.</tt><tt class="descname">CenterOfGeometry</tt><big>(</big><em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#CenterOfGeometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.CenterOfGeometry" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Timeseries.</code><code class="descname">CenterOfGeometry</code><span class="sig-paren">(</span><em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#CenterOfGeometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.CenterOfGeometry" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a timeseries that returns the center of geometry of a group of atoms</p>
 <blockquote>
 <div>t = CenterOfGeometry(atoms)</div></blockquote>
-<p><em>atoms</em> can be a list of <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>
-objects, or a <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></p>
+<p><em>atoms</em> can be a list of <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>
+objects, or a <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a></p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Timeseries.CenterOfMass">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Timeseries.</tt><tt class="descname">CenterOfMass</tt><big>(</big><em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#CenterOfMass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.CenterOfMass" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Timeseries.</code><code class="descname">CenterOfMass</code><span class="sig-paren">(</span><em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#CenterOfMass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.CenterOfMass" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a timeseries that returns the center of mass of a group of atoms</p>
 <blockquote>
 <div>t = CenterOfMass(atoms)</div></blockquote>
-<p><em>atoms</em> can be a list of <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>
-objects or a <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></p>
+<p><em>atoms</em> can be a list of <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>
+objects or a <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a></p>
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.Timeseries.WaterDipole">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.Timeseries.</tt><tt class="descname">WaterDipole</tt><big>(</big><em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#WaterDipole"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.WaterDipole" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.Timeseries.</code><code class="descname">WaterDipole</code><span class="sig-paren">(</span><em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/Timeseries.html#WaterDipole"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.Timeseries.WaterDipole" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a Timeseries that returns a timeseries for the bisector vector of a 3-site water</p>
 <blockquote>
 <div>d = WaterDipole(atoms)</div></blockquote>
-<p><em>atoms</em> must contain 3 <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>
+<p><em>atoms</em> must contain 3 <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>
 objects, either as a list or an
-<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>; the first one <em>must</em> be
+<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>; the first one <em>must</em> be
 the oxygen, the other two are the hydrogens.</p>
-<p>The vector <tt class="docutils literal"><span class="pre">d</span></tt>, multiplied by the partial charge on the oxygen atom
+<p>The vector <code class="docutils literal"><span class="pre">d</span></code>, multiplied by the partial charge on the oxygen atom
 (e.g. <em>q</em> = -0.0.834 for TIP3P water), gives the actual dipole moment.</p>
 <p>The vector is calculated from the positions of the oxygen atom
 (<span class="math">\(\mathbf{x}_{\text{O}}\)</span>) and the two hydrogen atoms
@@ -293,7 +294,7 @@ <h2>7.5.2. Timeseries of observables<a class="headerlink" href="#timeseries-of-o
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -308,11 +309,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="topologyobjects.html" title="7.4. Core Topology Objects — MDAnalysis.core.topologyobjects"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../core_modules.html" >7. Core modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../core_modules.html" >7. Core modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -322,7 +323,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/init.html b/package/doc/html/documentation_pages/core/init.html
index 45757765c4a..af56bf7560f 100644
--- a/package/doc/html/documentation_pages/core/init.html
+++ b/package/doc/html/documentation_pages/core/init.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>7.1. Core functions of MDAnalysis &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>7.1. Core functions of MDAnalysis &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="7. Core modules" href="../core_modules.html" />
     <link rel="next" title="7.2. Fundamental building blocks — MDAnalysis.core.AtomGroup" href="AtomGroup.html" />
     <link rel="prev" title="7. Core modules" href="../core_modules.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../core_modules.html" title="7. Core modules"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../core_modules.html" accesskey="U">7. Core modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../core_modules.html" accesskey="U">7. Core modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -77,13 +75,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">7. Core modules</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="AtomGroup.html"
-                        title="next chapter">7.2. Fundamental building blocks &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/core/init.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">7.2. Fundamental building blocks &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/core/init.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -102,16 +102,16 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.core.__init__"></span><div class="section" id="core-functions-of-mdanalysis">
 <h1>7.1. Core functions of MDAnalysis<a class="headerlink" href="#core-functions-of-mdanalysis" title="Permalink to this headline">¶</a></h1>
-<p>The basic class is an <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>;
+<p>The basic class is an <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>;
 the whole simulation is called the
-<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>. Selections are computed
-on an <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> and return another
-<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>.</p>
-<p><tt class="xref py py-mod docutils literal"><span class="pre">Timeseries</span></tt> are a convenient way to analyse trajectories.</p>
+<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>. Selections are computed
+on an <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> and return another
+<a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>.</p>
+<p><code class="xref py py-mod docutils literal"><span class="pre">Timeseries</span></code> are a convenient way to analyse trajectories.</p>
 <p>To get started, load the Universe:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">u</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">psffilename</span><span class="p">,</span><span class="n">dcdfilename</span><span class="p">)</span>
 </pre></div>
@@ -119,13 +119,13 @@ <h1>7.1. Core functions of MDAnalysis<a class="headerlink" href="#core-functions
 <p>A simple selection of all water oxygens within 4 A of the protein:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">water_shell</span> <span class="o">=</span> <span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&#39;name OH2 and around 4.0 protein&#39;</span><span class="p">)</span>
 <span class="n">water_shell</span><span class="o">.</span><span class="n">n_atoms</span>           <span class="c"># how many waters were selected</span>
-<span class="n">water_shell</span><span class="o">.</span><span class="n">totalMass</span><span class="p">()</span>       <span class="c"># their total mass</span>
+<span class="n">water_shell</span><span class="o">.</span><span class="n">total_mass</span><span class="p">()</span>       <span class="c"># their total mass</span>
 </pre></div>
 </div>
-<p><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt> instances have various methods that allow
+<p><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code> instances have various methods that allow
 calculation of simple properties. For more complicated analysis,
 obtain the coordinates as a numpy array</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">coords</span> <span class="o">=</span> <span class="n">water_shell</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">coords</span> <span class="o">=</span> <span class="n">water_shell</span><span class="o">.</span><span class="n">positions</span>
 </pre></div>
 </div>
 <p>and write your own Python code.</p>
@@ -133,9 +133,9 @@ <h1>7.1. Core functions of MDAnalysis<a class="headerlink" href="#core-functions
 <span id="flags-label"></span><h2>7.1.1. Flags<a class="headerlink" href="#flags" title="Permalink to this headline">¶</a></h2>
 <p>(This is an advanced topic and can probably be skipped by most people.)</p>
 <p>There are a number flags that influence how MDAnalysis behaves. They are accessible
-through the pseudo-dictionary <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt>.</p>
+through the pseudo-dictionary <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code>.</p>
 <p>The entries appear as &#8216;name&#8217;-&#8216;value&#8217; pairs. Flags check values and illegal ones
-raise a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt>. Documentation on all flags can be obtained with</p>
+raise a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code>. Documentation on all flags can be obtained with</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="k">print</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="o">.</span><span class="n">doc</span><span class="p">()</span>
 </pre></div>
 </div>
@@ -143,7 +143,7 @@ <h1>7.1. Core functions of MDAnalysis<a class="headerlink" href="#core-functions
 <h3>7.1.1.1. List of MDAnalysis flags with default values<a class="headerlink" href="#list-of-mdanalysis-flags-with-default-values" title="Permalink to this headline">¶</a></h3>
 <dl class="class">
 <dt id="MDAnalysis.core.__init__.flagsDocs">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.__init__.</tt><tt class="descname">flagsDocs</tt><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#flagsDocs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.flagsDocs" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.__init__.</code><code class="descname">flagsDocs</code><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#flagsDocs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.flagsDocs" title="Permalink to this definition">¶</a></dt>
 <dd><p><strong>use_periodic_selections</strong> = <em>True</em></p>
 <blockquote>
 <div><p>Determines if distance selections (AROUND, POINT) respect periodicity.</p>
@@ -177,7 +177,7 @@ <h3>7.1.1.1. List of MDAnalysis flags with default values<a class="headerlink" h
 <li>False, &#8216;never&#8217; - always use alternatives</li>
 </ul>
 <p>The preset value for MDAnalysis is &#8216;fast&#8217;.</p>
-<p><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.KDTree</span></tt> routines are significantly faster for some distance
+<p><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.KDTree</span></code> routines are significantly faster for some distance
 selections. However, they cannot deal with periodic boxes and thus ignore
 periodicity; if periodicity is crucial, disable KDTree routines with</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;use_KDTree_routines&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">False</span>
@@ -198,22 +198,22 @@ <h3>7.1.1.1. List of MDAnalysis flags with default values<a class="headerlink" h
 <p><strong>use_pbc</strong> = <em>False</em></p>
 <blockquote>
 <div><p>Choose whether to consider periodic boundary conditions when
-performing many <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> methods.
-This is set to <tt class="docutils literal"><span class="pre">False</span></tt> by default but can be enabled with:</p>
+performing many <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> methods.
+This is set to <code class="docutils literal"><span class="pre">False</span></code> by default but can be enabled with:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="p">[</span><span class="s">&#39;use_pbc&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span>
 </pre></div>
 </div>
 <p>Values for flag:</p>
 <ul class="simple">
-<li><tt class="docutils literal"><span class="pre">True</span></tt> - Move all atoms within the primary unit cell before calculation</li>
-<li><tt class="docutils literal"><span class="pre">False</span></tt> - Use coordinates as supplied</li>
+<li><code class="docutils literal"><span class="pre">True</span></code> - Move all atoms within the primary unit cell before calculation</li>
+<li><code class="docutils literal"><span class="pre">False</span></code> - Use coordinates as supplied</li>
 </ul>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
-<p class="last">Changing this to <tt class="docutils literal"><span class="pre">True</span></tt> changes the default behaviour of
-commonly used <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> methods
-such as <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass" title="MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass"><tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass()</span></tt></a>
-and <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry" title="MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry"><tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry()</span></tt></a>!</p>
+<p class="last">Changing this to <code class="docutils literal"><span class="pre">True</span></code> changes the default behaviour of
+commonly used <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> methods
+such as <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.center_of_mass" title="MDAnalysis.core.AtomGroup.AtomGroup.center_of_mass"><code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.center_of_mass()</span></code></a>
+and <a class="reference internal" href="AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry" title="MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry"><code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry()</span></code></a>!</p>
 </div>
 </div></blockquote>
 <p><strong>permissive_pdb_reader</strong> = <em>True</em></p>
@@ -225,17 +225,17 @@ <h3>7.1.1.1. List of MDAnalysis flags with default values<a class="headerlink" h
 <p>The Bio.PDB reader (value=``False``) can deal with &#8216;proper&#8217; PDB
 files from the Protein Databank that contain special PDB features
 such as insertion codes and it can auto-correct some common
-mistakes; see <tt class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></tt> for details. However, Bio.PDB has been
+mistakes; see <code class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></code> for details. However, Bio.PDB has been
 known to read some simulation system PDB files <strong>incompletely</strong>; a
 sure sign of problems is a warning that an atom has appeared twice
 in a residue.</p>
-<p>Therefore, the default for the PDB reader is <tt class="docutils literal"><span class="pre">True</span></tt>, which
+<p>Therefore, the default for the PDB reader is <code class="docutils literal"><span class="pre">True</span></code>, which
 selects the &#8220;primitive&#8221; (or &#8220;permissive&#8221;) reader
-<a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.PrimitivePDBReader</span></tt></a>, which
+<a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.PrimitivePDBReader</span></code></a>, which
 essentially just reads ATOM and HETATM lines and puts atoms in a
 list.</p>
 <p>One can manually switch between the two by providing the <em>permissive</em>
-keyword to <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt>.</p>
+keyword to <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code>.</p>
 </div></blockquote>
 <p><strong>convert_lengths</strong> = <em>True</em></p>
 <blockquote>
@@ -245,8 +245,8 @@ <h3>7.1.1.1. List of MDAnalysis flags with default values<a class="headerlink" h
 </div>
 <p>Some trajectories are in other length units than the MDAnalysis
 default (see the flag <em>length_unit</em>); e.g. Gromacs XTC and TRR
-trajectories are in nm. If <tt class="docutils literal"><span class="pre">True</span></tt> then coordinates are
-automatically converted, with <tt class="docutils literal"><span class="pre">False</span></tt> the coordinate values are
+trajectories are in nm. If <code class="docutils literal"><span class="pre">True</span></code> then coordinates are
+automatically converted, with <code class="docutils literal"><span class="pre">False</span></code> the coordinate values are
 presented as read from the trajectories.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
@@ -288,40 +288,40 @@ <h3>7.1.1.1. List of MDAnalysis flags with default values<a class="headerlink" h
 <h3>7.1.1.2. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h3>
 <dl class="data">
 <dt id="MDAnalysis.core.__init__.flags">
-<tt class="descclassname">MDAnalysis.core.__init__.</tt><tt class="descname">flags</tt><a class="headerlink" href="#MDAnalysis.core.__init__.flags" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.core.__init__.</code><code class="descname">flags</code><a class="headerlink" href="#MDAnalysis.core.__init__.flags" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.core.__init__.Flags">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.__init__.</tt><tt class="descname">Flags</tt><big>(</big><em>*args</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flags"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flags" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.__init__.</code><code class="descname">Flags</code><span class="sig-paren">(</span><em>*args</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flags"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flags" title="Permalink to this definition">¶</a></dt>
 <dd><p>Global registry of flags. Acts like a dict for item access.</p>
 <p>There are a number flags defined that influence how MDAnalysis behaves. They are
 accessible through the pseudo-dictionary</p>
 <blockquote>
-<div><tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></tt></div></blockquote>
+<div><code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.core.flags</span></code></div></blockquote>
 <p>The entries appear as &#8216;name&#8217;-&#8216;value&#8217; pairs. Flags check values and illegal ones
-raise a <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt>. Documentation on all flags can be obtained with</p>
+raise a <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code>. Documentation on all flags can be obtained with</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="k">print</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">flags</span><span class="o">.</span><span class="n">__doc__</span>
 </pre></div>
 </div>
-<p>New flags are added with the <a class="reference internal" href="#MDAnalysis.core.__init__.Flags.register" title="MDAnalysis.core.__init__.Flags.register"><tt class="xref py py-meth docutils literal"><span class="pre">Flags.register()</span></tt></a> method which takes a new <a class="reference internal" href="#MDAnalysis.core.__init__.Flag" title="MDAnalysis.core.__init__.Flag"><tt class="xref py py-class docutils literal"><span class="pre">Flag</span></tt></a>
+<p>New flags are added with the <a class="reference internal" href="#MDAnalysis.core.__init__.Flags.register" title="MDAnalysis.core.__init__.Flags.register"><code class="xref py py-meth docutils literal"><span class="pre">Flags.register()</span></code></a> method which takes a new <a class="reference internal" href="#MDAnalysis.core.__init__.Flag" title="MDAnalysis.core.__init__.Flag"><code class="xref py py-class docutils literal"><span class="pre">Flag</span></code></a>
 instance as an argument.</p>
-<p>For DEVELOPERS: Initialize Flags registry with a <em>list</em> of <a class="reference internal" href="#MDAnalysis.core.__init__.Flag" title="MDAnalysis.core.__init__.Flag"><tt class="xref py py-class docutils literal"><span class="pre">Flag</span></tt></a> instances.</p>
+<p>For DEVELOPERS: Initialize Flags registry with a <em>list</em> of <a class="reference internal" href="#MDAnalysis.core.__init__.Flag" title="MDAnalysis.core.__init__.Flag"><code class="xref py py-class docutils literal"><span class="pre">Flag</span></code></a> instances.</p>
 <dl class="method">
 <dt id="MDAnalysis.core.__init__.Flags.doc">
-<tt class="descname">doc</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flags.doc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flags.doc" title="Permalink to this definition">¶</a></dt>
+<code class="descname">doc</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flags.doc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flags.doc" title="Permalink to this definition">¶</a></dt>
 <dd><p>Shows doc strings for all flags.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.__init__.Flags.register">
-<tt class="descname">register</tt><big>(</big><em>flag</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flags.register"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flags.register" title="Permalink to this definition">¶</a></dt>
+<code class="descname">register</code><span class="sig-paren">(</span><em>flag</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flags.register"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flags.register" title="Permalink to this definition">¶</a></dt>
 <dd><p>Register a new Flag instance with the Flags registry.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.core.__init__.Flags.update">
-<tt class="descname">update</tt><big>(</big><em>*flags</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flags.update"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flags.update" title="Permalink to this definition">¶</a></dt>
+<code class="descname">update</code><span class="sig-paren">(</span><em>*flags</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flags.update"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flags.update" title="Permalink to this definition">¶</a></dt>
 <dd><p>Update Flags registry with a list of Flag instances.</p>
 </dd></dl>
 
@@ -329,7 +329,7 @@ <h3>7.1.1.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 
 <dl class="class">
 <dt id="MDAnalysis.core.__init__.Flag">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.core.__init__.</tt><tt class="descname">Flag</tt><big>(</big><em>name</em>, <em>default</em>, <em>mapping=None</em>, <em>doc=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flag"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flag" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.core.__init__.</code><code class="descname">Flag</code><span class="sig-paren">(</span><em>name</em>, <em>default</em>, <em>mapping=None</em>, <em>doc=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flag"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flag" title="Permalink to this definition">¶</a></dt>
 <dd><p>A Flag, essentially a variable that knows its default and legal values.</p>
 <p>Create a new flag which will be registered with FLags.</p>
 <blockquote>
@@ -338,7 +338,7 @@ <h3>7.1.1.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>name</em></dt>
 <dd><p class="first last">name of the flag, must be a legal python name</p>
 </dd>
@@ -347,15 +347,16 @@ <h3>7.1.1.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </dd>
 <dt><em>mapping</em></dt>
 <dd><p class="first last">dict that maps allowed input values to canonical values;
-if <tt class="docutils literal"><span class="pre">None</span></tt> then no argument checking will be performed and
+if <code class="docutils literal"><span class="pre">None</span></code> then no argument checking will be performed and
 all values are directly set.</p>
 </dd>
 <dt><em>doc</em></dt>
 <dd><p class="first">doc string; may contain string interpolation mappings for:</p>
-<div class="highlight-python"><pre>%%(name)s        name of the flag
+<div class="highlight-python"><div class="highlight"><pre>%%(name)s        name of the flag
 %%(default)r     default value
 %%(value)r       current value
-%%(mapping)r     mapping</pre>
+%%(mapping)r     mapping
+</pre></div>
 </div>
 <p class="last">Doc strings are generated dynamically and reflect the current state.</p>
 </dd>
@@ -366,8 +367,8 @@ <h3>7.1.1.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
 </table>
 <dl class="method">
 <dt id="MDAnalysis.core.__init__.Flag.prop">
-<tt class="descname">prop</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flag.prop"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flag.prop" title="Permalink to this definition">¶</a></dt>
-<dd><p>Use this for <tt class="docutils literal"><span class="pre">property(**flag.prop())</span></tt></p>
+<code class="descname">prop</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/core/__init__.html#Flag.prop"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.core.__init__.Flag.prop" title="Permalink to this definition">¶</a></dt>
+<dd><p>Use this for <code class="docutils literal"><span class="pre">property(**flag.prop())</span></code></p>
 </dd></dl>
 
 </dd></dl>
@@ -382,7 +383,7 @@ <h3>7.1.1.2. Classes<a class="headerlink" href="#classes" title="Permalink to th
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -397,11 +398,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../core_modules.html" title="7. Core modules"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../core_modules.html" >7. Core modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../core_modules.html" >7. Core modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -411,7 +412,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/topologyobjects.html b/package/doc/html/documentation_pages/core/topologyobjects.html
index 252d3aae070..53533570711 100644
--- a/package/doc/html/documentation_pages/core/topologyobjects.html
+++ b/package/doc/html/documentation_pages/core/topologyobjects.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>7.4. Core Topology Objects — MDAnalysis.core.topologyobjects &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>7.4. Core Topology Objects — MDAnalysis.core.topologyobjects &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="7. Core modules" href="../core_modules.html" />
     <link rel="next" title="7.5. Compute observable timeseries from trajectories — MDAnalysis.core.Timeseries" href="Timeseries.html" />
     <link rel="prev" title="7.3. Atom selection Hierarchy — MDAnalysis.core.Selection" href="Selection.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,27 +49,29 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="Selection.html" title="7.3. Atom selection Hierarchy — MDAnalysis.core.Selection"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../core_modules.html" accesskey="U">7. Core modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../core_modules.html" accesskey="U">7. Core modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="Selection.html"
-                        title="previous chapter">7.3. Atom selection Hierarchy &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.core.Selection</span></tt></a></p>
+                        title="previous chapter">7.3. Atom selection Hierarchy &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.Selection</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="Timeseries.html"
-                        title="next chapter">7.5. Compute observable timeseries from trajectories &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.core.Timeseries</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/core/topologyobjects.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">7.5. Compute observable timeseries from trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.Timeseries</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/core/topologyobjects.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,10 +90,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.core.topologyobjects"></span><div class="section" id="core-topology-objects-mdanalysis-core-topologyobjects">
-<h1>7.4. Core Topology Objects &#8212; <a class="reference internal" href="#module-MDAnalysis.core.topologyobjects" title="MDAnalysis.core.topologyobjects"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.topologyobjects</span></tt></a><a class="headerlink" href="#core-topology-objects-mdanalysis-core-topologyobjects" title="Permalink to this headline">¶</a></h1>
+<h1>7.4. Core Topology Objects &#8212; <a class="reference internal" href="#module-MDAnalysis.core.topologyobjects" title="MDAnalysis.core.topologyobjects"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.topologyobjects</span></code></a><a class="headerlink" href="#core-topology-objects-mdanalysis-core-topologyobjects" title="Permalink to this headline">¶</a></h1>
 <p>The building blocks for MDAnalysis&#8217; description of topology</p>
 </div>
 
@@ -103,7 +103,7 @@ <h1>7.4. Core Topology Objects &#8212; <a class="reference internal" href="#modu
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -118,11 +118,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="Selection.html" title="7.3. Atom selection Hierarchy — MDAnalysis.core.Selection"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../core_modules.html" >7. Core modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../core_modules.html" >7. Core modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -132,7 +132,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core_modules.html b/package/doc/html/documentation_pages/core_modules.html
index 1f73c2652ab..84551546f00 100644
--- a/package/doc/html/documentation_pages/core_modules.html
+++ b/package/doc/html/documentation_pages/core_modules.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>7. Core modules &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>7. Core modules &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="7.1. Core functions of MDAnalysis" href="core/init.html" />
     <link rel="prev" title="6.6. Base classes for the selection writers" href="selections/base.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -50,10 +48,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="selections/base.html" title="6.6. Base classes for the selection writers"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../index.html">
               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -64,12 +62,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="core/init.html"
                         title="next chapter">7.1. Core functions of MDAnalysis</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/core_modules.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/core_modules.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -88,22 +88,22 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="core-modules">
 <h1>7. Core modules<a class="headerlink" href="#core-modules" title="Permalink to this headline">¶</a></h1>
-<p>The <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core</span></tt> modules contain functionality essential for
+<p>The <code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core</span></code> modules contain functionality essential for
 MDAnalysis, such as the central data structures in
-<a class="reference internal" href="core/AtomGroup.html#module-MDAnalysis.core.AtomGroup" title="MDAnalysis.core.AtomGroup"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></tt></a> or the selection definitions and
-parsing in <a class="reference internal" href="core/Selection.html#module-MDAnalysis.core.Selection" title="MDAnalysis.core.Selection"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.Selection</span></tt></a>.</p>
+<a class="reference internal" href="core/AtomGroup.html#module-MDAnalysis.core.AtomGroup" title="MDAnalysis.core.AtomGroup"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></code></a> or the selection definitions and
+parsing in <a class="reference internal" href="core/Selection.html#module-MDAnalysis.core.Selection" title="MDAnalysis.core.Selection"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.Selection</span></code></a>.</p>
 <p class="rubric">Contents</p>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="core/init.html">7.1. Core functions of MDAnalysis</a></li>
-<li class="toctree-l1"><a class="reference internal" href="core/AtomGroup.html">7.2. Fundamental building blocks &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="core/Selection.html">7.3. Atom selection Hierarchy &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.core.Selection</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="core/topologyobjects.html">7.4. Core Topology Objects &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.core.topologyobjects</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="core/Timeseries.html">7.5. Compute observable timeseries from trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.core.Timeseries</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="core/AtomGroup.html">7.2. Fundamental building blocks &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.AtomGroup</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="core/Selection.html">7.3. Atom selection Hierarchy &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.Selection</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="core/topologyobjects.html">7.4. Core Topology Objects &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.topologyobjects</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="core/Timeseries.html">7.5. Compute observable timeseries from trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.Timeseries</span></code></a></li>
 </ul>
 </div>
 </div>
@@ -114,7 +114,7 @@ <h1>7. Core modules<a class="headerlink" href="#core-modules" title="Permalink t
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -129,10 +129,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="selections/base.html" title="6.6. Base classes for the selection writers"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -142,7 +142,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/exceptions.html b/package/doc/html/documentation_pages/exceptions.html
index c58885f4616..052de299d1f 100644
--- a/package/doc/html/documentation_pages/exceptions.html
+++ b/package/doc/html/documentation_pages/exceptions.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>12. Custom exceptions and warnings — MDAnalysis.exceptions &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>12. Custom exceptions and warnings — MDAnalysis.exceptions &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="13. References" href="references.html" />
     <link rel="prev" title="11. Constants and unit conversion — MDAnalysis.units" href="units.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -50,26 +48,28 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="units.html" title="11. Constants and unit conversion — MDAnalysis.units"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../index.html">
               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="units.html"
-                        title="previous chapter">11. Constants and unit conversion &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.units</span></tt></a></p>
+                        title="previous chapter">11. Constants and unit conversion &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.units</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="references.html"
                         title="next chapter">13. References</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/exceptions.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/exceptions.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -88,68 +88,69 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.exceptions"></span><div class="section" id="custom-exceptions-and-warnings-mdanalysis-exceptions">
-<h1>12. Custom exceptions and warnings &#8212; <a class="reference internal" href="#module-MDAnalysis.exceptions" title="MDAnalysis.exceptions"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.exceptions</span></tt></a><a class="headerlink" href="#custom-exceptions-and-warnings-mdanalysis-exceptions" title="Permalink to this headline">¶</a></h1>
+<h1>12. Custom exceptions and warnings &#8212; <a class="reference internal" href="#module-MDAnalysis.exceptions" title="MDAnalysis.exceptions"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.exceptions</span></code></a><a class="headerlink" href="#custom-exceptions-and-warnings-mdanalysis-exceptions" title="Permalink to this headline">¶</a></h1>
 <dl class="exception">
 <dt id="MDAnalysis.exceptions.ApplicationError">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.exceptions.</tt><tt class="descname">ApplicationError</tt><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#ApplicationError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.ApplicationError" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.exceptions.</code><code class="descname">ApplicationError</code><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#ApplicationError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.ApplicationError" title="Permalink to this definition">¶</a></dt>
 <dd><p>Raised when an external application failed.</p>
 <p>The error code is specific for the application.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="exception">
 <dt id="MDAnalysis.exceptions.ConversionWarning">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.exceptions.</tt><tt class="descname">ConversionWarning</tt><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#ConversionWarning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.ConversionWarning" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.exceptions.</code><code class="descname">ConversionWarning</code><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#ConversionWarning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.ConversionWarning" title="Permalink to this definition">¶</a></dt>
 <dd><p>Warning indicating a problem with converting between units.</p>
 </dd></dl>
 
 <dl class="exception">
 <dt id="MDAnalysis.exceptions.FileFormatWarning">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.exceptions.</tt><tt class="descname">FileFormatWarning</tt><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#FileFormatWarning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.FileFormatWarning" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.exceptions.</code><code class="descname">FileFormatWarning</code><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#FileFormatWarning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.FileFormatWarning" title="Permalink to this definition">¶</a></dt>
 <dd><p>Warning indicating possible problems with a file format.</p>
 </dd></dl>
 
 <dl class="exception">
 <dt id="MDAnalysis.exceptions.FinishTimeException">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.exceptions.</tt><tt class="descname">FinishTimeException</tt><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#FinishTimeException"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.FinishTimeException" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.exceptions.</code><code class="descname">FinishTimeException</code><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#FinishTimeException"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.FinishTimeException" title="Permalink to this definition">¶</a></dt>
 <dd><p>For Issue 188.</p>
 </dd></dl>
 
 <dl class="exception">
 <dt id="MDAnalysis.exceptions.MissingDataWarning">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.exceptions.</tt><tt class="descname">MissingDataWarning</tt><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#MissingDataWarning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.MissingDataWarning" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.exceptions.</code><code class="descname">MissingDataWarning</code><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#MissingDataWarning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.MissingDataWarning" title="Permalink to this definition">¶</a></dt>
 <dd><p>Warning indicating is that required data are missing.</p>
 </dd></dl>
 
 <dl class="exception">
 <dt id="MDAnalysis.exceptions.NoDataError">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.exceptions.</tt><tt class="descname">NoDataError</tt><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#NoDataError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.NoDataError" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.exceptions.</code><code class="descname">NoDataError</code><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#NoDataError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.NoDataError" title="Permalink to this definition">¶</a></dt>
 <dd><p>Raised when empty input is not allowed or required data are missing.</p>
 </dd></dl>
 
 <dl class="exception">
 <dt id="MDAnalysis.exceptions.SelectionError">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.exceptions.</tt><tt class="descname">SelectionError</tt><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#SelectionError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.SelectionError" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.exceptions.</code><code class="descname">SelectionError</code><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#SelectionError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.SelectionError" title="Permalink to this definition">¶</a></dt>
 <dd><p>Raised when a atom selection failed.</p>
 </dd></dl>
 
 <dl class="exception">
 <dt id="MDAnalysis.exceptions.SelectionWarning">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.exceptions.</tt><tt class="descname">SelectionWarning</tt><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#SelectionWarning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.SelectionWarning" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.exceptions.</code><code class="descname">SelectionWarning</code><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#SelectionWarning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.SelectionWarning" title="Permalink to this definition">¶</a></dt>
 <dd><p>Warning indicating a possible problem with a selection.</p>
 </dd></dl>
 
 <dl class="exception">
 <dt id="MDAnalysis.exceptions.StreamWarning">
-<em class="property">exception </em><tt class="descclassname">MDAnalysis.exceptions.</tt><tt class="descname">StreamWarning</tt><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#StreamWarning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.StreamWarning" title="Permalink to this definition">¶</a></dt>
+<em class="property">exception </em><code class="descclassname">MDAnalysis.exceptions.</code><code class="descname">StreamWarning</code><a class="reference internal" href="../_modules/MDAnalysis/exceptions.html#StreamWarning"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.exceptions.StreamWarning" title="Permalink to this definition">¶</a></dt>
 <dd><p>Warning indicating a possible problem with a stream.</p>
-<p><a class="reference internal" href="#MDAnalysis.exceptions.StreamWarning" title="MDAnalysis.exceptions.StreamWarning"><tt class="xref py py-exc docutils literal"><span class="pre">StreamWarning</span></tt></a> is used when streams are substituted for simple access
+<p><a class="reference internal" href="#MDAnalysis.exceptions.StreamWarning" title="MDAnalysis.exceptions.StreamWarning"><code class="xref py py-exc docutils literal"><span class="pre">StreamWarning</span></code></a> is used when streams are substituted for simple access
 by filename (see in particular
-<a class="reference internal" href="lib/util.html#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><tt class="xref py py-class docutils literal"><span class="pre">NamedStream</span></tt></a>). This does not work everywhere
+<a class="reference internal" href="lib/util.html#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><code class="xref py py-class docutils literal"><span class="pre">NamedStream</span></code></a>). This does not work everywhere
 in MDAnalysis (yet).</p>
 </dd></dl>
 
@@ -161,7 +162,7 @@ <h1>12. Custom exceptions and warnings &#8212; <a class="reference internal" hre
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -176,10 +177,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="units.html" title="11. Constants and unit conversion — MDAnalysis.units"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -189,7 +190,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/lib/NeighborSearch.html b/package/doc/html/documentation_pages/lib/NeighborSearch.html
new file mode 100644
index 00000000000..15f7ad95527
--- /dev/null
+++ b/package/doc/html/documentation_pages/lib/NeighborSearch.html
@@ -0,0 +1,195 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>9.3. Neighbor Search wrapper for MDAnalysis — :mod: MDAnalysis.lib.NeighborSearch &mdash; MDAnalysis 0.11.0 documentation</title>
+    
+    <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
+    <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
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+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../../',
+        VERSION:     '0.11.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="../../_static/jquery.js"></script>
+    <script type="text/javascript" src="../../_static/underscore.js"></script>
+    <script type="text/javascript" src="../../_static/doctools.js"></script>
+    <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <link rel="search" type="application/opensearchdescription+xml"
+          title="Search within MDAnalysis 0.11.0 documentation"
+          href="../../_static/opensearch.xml"/>
+    <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
+    <link rel="up" title="9. MDAnalysis library" href="../lib_modules.html" />
+    <link rel="next" title="9.4. Setting up logging — MDAnalysis.lib.log" href="log.html" />
+    <link rel="prev" title="9.2. Distance calculation library — MDAnalysis.lib._distances" href="_distances.html" /> 
+  </head>
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="../../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="right" >
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+             accesskey="N">next</a> |</li>
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+          <a href="_distances.html" title="9.2. Distance calculation library — MDAnalysis.lib._distances"
+             accesskey="P">previous</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
+      </ul>
+    </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+            <p class="logo"><a href="../../index.html">
+              <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
+            </a></p>
+  <h4>Previous topic</h4>
+  <p class="topless"><a href="_distances.html"
+                        title="previous chapter">9.2. Distance calculation library &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib._distances</span></code></a></p>
+  <h4>Next topic</h4>
+  <p class="topless"><a href="log.html"
+                        title="next chapter">9.4. Setting up logging &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.log</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/lib/NeighborSearch.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
+  <h3>Quick search</h3>
+    <form class="search" action="../../search.html" method="get">
+      <input type="text" name="q" />
+      <input type="submit" value="Go" />
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+    <p class="searchtip" style="font-size: 90%">
+    Enter search terms or a module, class or function name.
+    </p>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <span class="target" id="module-MDAnalysis.lib.NeighborSearch"></span><div class="section" id="neighbor-search-wrapper-for-mdanalysis-mod-mdanalysis-lib-neighborsearch">
+<h1>9.3. Neighbor Search wrapper for MDAnalysis &#8212; :mod: <cite>MDAnalysis.lib.NeighborSearch</cite><a class="headerlink" href="#neighbor-search-wrapper-for-mdanalysis-mod-mdanalysis-lib-neighborsearch" title="Permalink to this headline">¶</a></h1>
+<p>This module contains classes that allow neighbor searches directly with
+<cite>AtomGroup</cite> objects from <cite>MDAnalysis</cite>.</p>
+<dl class="class">
+<dt id="MDAnalysis.lib.NeighborSearch.AtomNeighborSearch">
+<em class="property">class </em><code class="descclassname">MDAnalysis.lib.NeighborSearch.</code><code class="descname">AtomNeighborSearch</code><span class="sig-paren">(</span><em>atom_group</em>, <em>bucket_size=10</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/NeighborSearch.html#AtomNeighborSearch"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.NeighborSearch.AtomNeighborSearch" title="Permalink to this definition">¶</a></dt>
+<dd><p>This class can be used to find all atoms/residues/segements within the
+radius of a given query position.</p>
+<p>This class is using the BioPython KDTree for the neighborsearch. This class
+also does not apply PBC to the distance calculattions. So you have to ensure
+yourself that the trajectory has been corrected for PBC artifacts.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>atom_list</em></dt>
+<dd><p class="first last">list of atoms (:class: <cite>~MDAnalysis.core.AtomGroup.AtomGroup</cite>)</p>
+</dd>
+<dt><em>bucket_size</em></dt>
+<dd><p class="first last">Number of entries in leafs of the KDTree. If you suffer poor
+performance you can play around with this number. Increasing the
+<cite>bucket_size</cite> will speed up the construction of the KDTree but
+slow down the search.</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
+<dt id="MDAnalysis.lib.NeighborSearch.AtomNeighborSearch.search">
+<code class="descname">search</code><span class="sig-paren">(</span><em>atoms</em>, <em>radius</em>, <em>level='A'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/NeighborSearch.html#AtomNeighborSearch.search"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.NeighborSearch.AtomNeighborSearch.search" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return all atoms/residues/segments that are within <em>radius</em> of the
+atoms in <em>atoms</em>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>atoms</em></dt>
+<dd><p class="first last">list of atoms (:class: <cite>~MDAnalysis.core.AtomGroup.AtomGroup</cite>)</p>
+</dd>
+<dt><em>radius</em></dt>
+<dd><p class="first last">float. Radius for search in Angstrom.</p>
+</dd>
+<dt><em>level</em> (optional)</dt>
+<dd><p class="first last">char (A, R, S). Return atoms(A), residues(R) or segments(S) within
+<em>radius</em> of <em>atoms</em>.</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="../../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="right" >
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+             >next</a> |</li>
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+          <a href="_distances.html" title="9.2. Distance calculation library — MDAnalysis.lib._distances"
+             >previous</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
+    Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
+    David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
+    Lennard van der Feltz, Philip Fowler, Joseph Goose, Richard J. Gowers, Lukas Grossar,
+    Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon, Alex Nesterenko,
+    Manuel Nuno Melo, Caio S. Souza, Danny Parton, Joshua L. Phillips, Tyler Reddy,
+    Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
+    Zhuyi Xue, Carlos Yáñez S.,
+    and Oliver Beckstein.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
+    </div>
+  </body>
+</html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/lib/_distances.html b/package/doc/html/documentation_pages/lib/_distances.html
index 1aac50f2734..e3990c22520 100644
--- a/package/doc/html/documentation_pages/lib/_distances.html
+++ b/package/doc/html/documentation_pages/lib/_distances.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>9.2. Distance calculation library — MDAnalysis.lib._distances &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>9.2. Distance calculation library — MDAnalysis.lib._distances &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="9. MDAnalysis library" href="../lib_modules.html" />
-    <link rel="next" title="9.3. KDTree module" href="KDTree_modules.html" />
+    <link rel="next" title="9.3. Neighbor Search wrapper for MDAnalysis — :mod: MDAnalysis.lib.NeighborSearch" href="NeighborSearch.html" />
     <link rel="prev" title="9.1. Fast distance array computation — MDAnalysis.lib.distances" href="distances.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -46,32 +44,34 @@ <h3>Navigation</h3>
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="KDTree_modules.html" title="9.3. KDTree module"
+          <a href="NeighborSearch.html" title="9.3. Neighbor Search wrapper for MDAnalysis — :mod: MDAnalysis.lib.NeighborSearch"
              accesskey="N">next</a> |</li>
         <li class="right" >
           <a href="distances.html" title="9.1. Fast distance array computation — MDAnalysis.lib.distances"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="distances.html"
-                        title="previous chapter">9.1. Fast distance array computation &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.distances</span></tt></a></p>
+                        title="previous chapter">9.1. Fast distance array computation &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.distances</span></code></a></p>
   <h4>Next topic</h4>
-  <p class="topless"><a href="KDTree_modules.html"
-                        title="next chapter">9.3. KDTree module</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/lib/_distances.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <p class="topless"><a href="NeighborSearch.html"
+                        title="next chapter">9.3. Neighbor Search wrapper for MDAnalysis &#8212; :mod: <cite>MDAnalysis.lib.NeighborSearch</cite></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/lib/_distances.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,10 +90,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.lib._distances"></span><div class="section" id="distance-calculation-library-mdanalysis-lib-distances">
-<h1>9.2. Distance calculation library &#8212; <a class="reference internal" href="#module-MDAnalysis.lib._distances" title="MDAnalysis.lib._distances"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib._distances</span></tt></a><a class="headerlink" href="#distance-calculation-library-mdanalysis-lib-distances" title="Permalink to this headline">¶</a></h1>
+<h1>9.2. Distance calculation library &#8212; <a class="reference internal" href="#module-MDAnalysis.lib._distances" title="MDAnalysis.lib._distances"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib._distances</span></code></a><a class="headerlink" href="#distance-calculation-library-mdanalysis-lib-distances" title="Permalink to this headline">¶</a></h1>
 <p>Serial versions of all distance calculations</p>
 </div>
 
@@ -103,7 +103,7 @@ <h1>9.2. Distance calculation library &#8212; <a class="reference internal" href
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -113,16 +113,16 @@ <h3>Navigation</h3>
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="KDTree_modules.html" title="9.3. KDTree module"
+          <a href="NeighborSearch.html" title="9.3. Neighbor Search wrapper for MDAnalysis — :mod: MDAnalysis.lib.NeighborSearch"
              >next</a> |</li>
         <li class="right" >
           <a href="distances.html" title="9.1. Fast distance array computation — MDAnalysis.lib.distances"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -132,7 +132,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/lib/distances.html b/package/doc/html/documentation_pages/lib/distances.html
index a477ea34f68..1e13ca70705 100644
--- a/package/doc/html/documentation_pages/lib/distances.html
+++ b/package/doc/html/documentation_pages/lib/distances.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>9.1. Fast distance array computation — MDAnalysis.lib.distances &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>9.1. Fast distance array computation — MDAnalysis.lib.distances &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="9. MDAnalysis library" href="../lib_modules.html" />
     <link rel="next" title="9.2. Distance calculation library — MDAnalysis.lib._distances" href="_distances.html" />
     <link rel="prev" title="9. MDAnalysis library" href="../lib_modules.html" /> 
   </head>
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../lib_modules.html" title="9. MDAnalysis library"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">9.1. Fast distance array computation &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.distances</span></tt></a><ul>
+<li><a class="reference internal" href="#">9.1. Fast distance array computation &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.distances</span></code></a><ul>
 <li><a class="reference internal" href="#functions">9.1.1. Functions</a></li>
 </ul>
 </li>
@@ -73,13 +71,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">9. MDAnalysis library</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="_distances.html"
-                        title="next chapter">9.2. Distance calculation library &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.lib._distances</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/lib/distances.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">9.2. Distance calculation library &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib._distances</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/lib/distances.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,30 +98,30 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.lib.distances"></span><div class="section" id="fast-distance-array-computation-mdanalysis-lib-distances">
-<h1>9.1. Fast distance array computation &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.distances" title="MDAnalysis.lib.distances"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.distances</span></tt></a><a class="headerlink" href="#fast-distance-array-computation-mdanalysis-lib-distances" title="Permalink to this headline">¶</a></h1>
+<h1>9.1. Fast distance array computation &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.distances" title="MDAnalysis.lib.distances"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.distances</span></code></a><a class="headerlink" href="#fast-distance-array-computation-mdanalysis-lib-distances" title="Permalink to this headline">¶</a></h1>
 <p>Fast C-routines to calculate distance arrays from coordinate arrays.</p>
 <div class="section" id="functions">
 <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.lib.distances.distance_array">
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">distance_array</tt><big>(</big><em>reference</em>, <em>configuation</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#distance_array"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.distance_array" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">distance_array</code><span class="sig-paren">(</span><em>reference</em>, <em>configuation</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#distance_array"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.distance_array" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate all distances between a reference set and another configuration.</p>
 <p>If there are <em>i</em> positions in reference, and <em>j</em> positions in configuration,
 will calculate a <em>i</em> x <em>j</em> array of distances
 If an <em>box</em> is supplied then a minimum image convention is used when
 calculating distances.</p>
-<p>If a 2D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with the shape <tt class="docutils literal"><span class="pre">(len(reference),</span>
-<span class="pre">len(configuration))</span></tt> is provided in <em>result</em> then this preallocated array is
+<p>If a 2D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with the shape <code class="docutils literal"><span class="pre">(len(reference),</span>
+<span class="pre">len(configuration))</span></code> is provided in <em>result</em> then this preallocated array is
 filled. This can speed up calculations.</p>
 <p>d = distance_array(reference, configuration[,box[,result=d]])</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>reference</em></dt>
 <dd><p class="first last">reference coordinate array (must be numpy.float32)</p>
 </dd>
@@ -130,21 +130,21 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">cell dimensions (minimum image convention is applied)
-or None [<tt class="docutils literal"><span class="pre">None</span></tt>].
+or None [<code class="docutils literal"><span class="pre">None</span></code>].
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
 <dd><p class="first last">optional preallocated result array which must have the
 shape (len(ref), len(conf)) and dtype=numpy.float64.
 Avoids creating the array which saves time when the function
-is called repeatedly. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+is called repeatedly. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>d</em></dt>
 <dd><p class="first last">(len(reference),len(configuration)) numpy array with the distances d[i,j]
 between reference coordinates i and configuration coordinates j</p>
@@ -163,38 +163,38 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.distances.self_distance_array">
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">self_distance_array</tt><big>(</big><em>reference</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#self_distance_array"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.self_distance_array" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">self_distance_array</code><span class="sig-paren">(</span><em>reference</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#self_distance_array"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.self_distance_array" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate all distances within a configuration <em>reference</em>.</p>
 <p>If a <em>box</em> is supplied then a minimum image convention is used before
 calculating distances.</p>
-<p>If a 1D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with the shape
-<tt class="docutils literal"><span class="pre">(N*(N-1)/2)</span></tt> is provided in <em>result</em> then this preallocated array
+<p>If a 1D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with the shape
+<code class="docutils literal"><span class="pre">(N*(N-1)/2)</span></code> is provided in <em>result</em> then this preallocated array
 is filled. This can speed up calculations.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>ref</em></dt>
 <dd><p class="first last">reference coordinate array with N=len(ref) coordinates</p>
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">cell dimensions (minimum image convention is applied)
-or None [<tt class="docutils literal"><span class="pre">None</span></tt>]
+or None [<code class="docutils literal"><span class="pre">None</span></code>]
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
 <dd><p class="first last">optional preallocated result array which must have the shape
-(N*(N-1)/2,) and dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt>. Avoids creating
+(N*(N-1)/2,) and dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code>. Avoids creating
 the array which saves time when the function is called
-repeatedly. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+repeatedly. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>d</em></dt>
 <dd><p class="first">N*(N-1)/2 numpy 1D array with the distances dist[i,j] between ref
 coordinates i and j at position d[k]. Loop through d:</p>
@@ -219,17 +219,18 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.distances.calc_bonds">
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">calc_bonds</tt><big>(</big><em>atom1</em>, <em>atom2</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.calc_bonds" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">calc_bonds</code><span class="sig-paren">(</span><em>atom1</em>, <em>atom2</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.calc_bonds" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate all distances between a pair of atoms.  <em>atom1</em> and <em>atom2</em> are both
 arrays of coordinates, where atom1[i] and atom2[i] represent a bond.</p>
 <p>In comparison to distance_array and self_distance_array which calculate distances
 between all combinations of coordinates, calc_bonds can be used to calculate distance
 between pairs of objects, similar to:</p>
-<div class="highlight-python"><pre>numpy.linalg.norm(a - b) for a, b in zip(coords1, coords2)</pre>
+<div class="highlight-python"><div class="highlight"><pre>numpy.linalg.norm(a - b) for a, b in zip(coords1, coords2)
+</pre></div>
 </div>
 <p>The optional argument <em>box</em> applies minimum image convention if supplied.
 <em>box</em> can be either orthogonal or triclinic</p>
-<p>If a 1D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with <tt class="docutils literal"><span class="pre">len(atom1)</span></tt> elements is
+<p>If a 1D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with <code class="docutils literal"><span class="pre">len(atom1)</span></code> elements is
 provided in <em>result</em> then this preallocated array is filled. This can speed
 up calculations.</p>
 <p>bondlengths = calc_bonds(coords1, coords2 [, box [,result=bondlengths]])</p>
@@ -237,7 +238,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>coords1</em></dt>
 <dd><p class="first last">An array of coordinates for one half of the bond</p>
 </dd>
@@ -247,7 +248,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 <dt><em>box</em></dt>
 <dd><p class="first last">Unit cell information if periodic boundary conditions are required [None]
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
@@ -258,7 +259,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>bondlengths</em></dt>
 <dd><p class="first last">Numpy array with the length between each pair in coords1 and coords2</p>
 </dd>
@@ -267,20 +268,21 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.distances.calc_angles">
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">calc_angles</tt><big>(</big><em>atom1</em>, <em>atom2</em>, <em>atom3</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_angles"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.calc_angles" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">calc_angles</code><span class="sig-paren">(</span><em>atom1</em>, <em>atom2</em>, <em>atom3</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_angles"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.calc_angles" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculates the angle formed between three atoms, over a list of coordinates.
 All <em>atom</em> inputs are lists of coordinates of equal length, with <em>atom2</em>
 representing the apex of the angle.</p>
-<p>If a 1D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with <tt class="docutils literal"><span class="pre">len(atom1)</span></tt> elements is
+<p>If a 1D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with <code class="docutils literal"><span class="pre">len(atom1)</span></code> elements is
 provided in <em>result</em> then this preallocated array is filled. This can speed
 up calculations.</p>
-<p>The optional argument <tt class="docutils literal"><span class="pre">box</span></tt> ensures that periodic boundaries are taken into account when
+<p>The optional argument <code class="docutils literal"><span class="pre">box</span></code> ensures that periodic boundaries are taken into account when
 constructing the connecting vectors between atoms, ie that the vector between atoms 1 &amp; 2
 goes between coordinates in the same image.</p>
 <p>angles = calc_angles(coords1, coords2, coords3, [[box=None],result=angles])</p>
@@ -288,7 +290,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>coords1</em></dt>
 <dd><p class="first last">coordinate array of one side of angles</p>
 </dd>
@@ -303,7 +305,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 atoms respect minimum image convention.  This is import when the angle might
 be between atoms in different images.
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
@@ -313,7 +315,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>angles</em></dt>
 <dd><p class="first last">A numpy.array of angles in radians</p>
 </dd>
@@ -322,28 +324,31 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Added optional box argument to account for periodic boundaries in calculation</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Added optional box argument to account for periodic boundaries in calculation</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.distances.calc_dihedrals">
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">calc_dihedrals</tt><big>(</big><em>atom1</em>, <em>atom2</em>, <em>atom3</em>, <em>atom4</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_dihedrals"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.calc_dihedrals" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">calc_dihedrals</code><span class="sig-paren">(</span><em>atom1</em>, <em>atom2</em>, <em>atom3</em>, <em>atom4</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_dihedrals"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.calc_dihedrals" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate the dihedral angle formed by four atoms, over a list of coordinates.</p>
 <p>Dihedral angle around axis connecting atoms 1 and 2 (i.e. the angle
 between the planes spanned by atoms (0,1,2) and (1,2,3)):</p>
-<div class="highlight-python"><pre>        3
+<div class="highlight-python"><div class="highlight"><pre>        3
         |
   1-----2
  /
-0</pre>
+0
+</pre></div>
 </div>
-<p>If a 1D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with <tt class="docutils literal"><span class="pre">len(atom1)</span></tt> elements is
+<p>If a 1D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with <code class="docutils literal"><span class="pre">len(atom1)</span></code> elements is
 provided in <em>result</em> then this preallocated array is filled. This can speed
 up calculations.</p>
-<p>The optional argument <tt class="docutils literal"><span class="pre">box</span></tt> ensures that periodic boundaries are taken into
+<p>The optional argument <code class="docutils literal"><span class="pre">box</span></code> ensures that periodic boundaries are taken into
 account when constructing the connecting vectors between atoms, ie that the vector
 between atoms 1 &amp; 2 goes between coordinates in the same image.</p>
 <p>angles = calc_dihedrals(coords1, coords2, coords3, coords4 [,box=box, result=angles])</p>
@@ -351,7 +356,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>coords1</em></dt>
 <dd><p class="first last">coordinate array of 1st atom in dihedrals</p>
 </dd>
@@ -369,7 +374,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 between atoms respect minimum image convention.  This is import when the
 angle might be between atoms in different images.
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
@@ -379,7 +384,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>angles</em></dt>
 <dd><p class="first last">A numpy.array of angles in radians</p>
 </dd>
@@ -388,35 +393,40 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Added optional box argument to account for periodic boundaries in calculation</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Added optional box argument to account for periodic boundaries in calculation</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Renamed from calc_torsions to calc_dihedrals</p>
+</div>
 </dd></dl>
 
 <dl class="function">
-<dt id="MDAnalysis.lib.distances.applyPBC">
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">applyPBC</tt><big>(</big><em>coordinates</em>, <em>box</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#applyPBC"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.applyPBC" title="Permalink to this definition">¶</a></dt>
+<dt id="MDAnalysis.lib.distances.apply_PBC">
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">apply_PBC</code><span class="sig-paren">(</span><em>coordinates</em>, <em>box</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#apply_PBC"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.apply_PBC" title="Permalink to this definition">¶</a></dt>
 <dd><p>Moves a set of coordinates to all be within the primary unit cell</p>
-<p>newcoords = applyPBC(coords, box)</p>
+<p>newcoords = apply_PBC(coords, box)</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>coords</em></dt>
 <dd><p class="first last">coordinate array (of type numpy.float32)</p>
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">box dimensions, can be either orthogonal or triclinic information
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>newcoords</em></dt>
 <dd><p class="first last">coordinates that are now all within the primary unit cell,
 as defined by box</p>
@@ -426,34 +436,35 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.distances.transform_RtoS">
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">transform_RtoS</tt><big>(</big><em>coordinates</em>, <em>box</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#transform_RtoS"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.transform_RtoS" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">transform_RtoS</code><span class="sig-paren">(</span><em>coordinates</em>, <em>box</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#transform_RtoS"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.transform_RtoS" title="Permalink to this definition">¶</a></dt>
 <dd><p>Transform an array of coordinates from real space to S space (aka lambda space)</p>
 <p>S space represents fractional space within the unit cell for this system</p>
-<p>Reciprocal operation to <a class="reference internal" href="#MDAnalysis.lib.distances.transform_StoR" title="MDAnalysis.lib.distances.transform_StoR"><tt class="xref py py-meth docutils literal"><span class="pre">transform_StoR()</span></tt></a></p>
+<p>Reciprocal operation to <a class="reference internal" href="#MDAnalysis.lib.distances.transform_StoR" title="MDAnalysis.lib.distances.transform_StoR"><code class="xref py py-meth docutils literal"><span class="pre">transform_StoR()</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>inputcoords</em></dt>
 <dd><p class="first last">An n x 3 array of coordinate data, of type np.float32</p>
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">The unitcell dimesions for this system
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>outcoords</em></dt>
 <dd><p class="first last">An n x 3 array of fractional coordiantes</p>
 </dd>
@@ -466,28 +477,28 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.distances.transform_StoR">
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">transform_StoR</tt><big>(</big><em>coordinates</em>, <em>box</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#transform_StoR"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.transform_StoR" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">transform_StoR</code><span class="sig-paren">(</span><em>coordinates</em>, <em>box</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#transform_StoR"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.distances.transform_StoR" title="Permalink to this definition">¶</a></dt>
 <dd><p>Transform an array of coordinates from S space into real space.</p>
 <p>S space represents fractional space within the unit cell for this system</p>
-<p>Reciprocal operation to <a class="reference internal" href="#MDAnalysis.lib.distances.transform_RtoS" title="MDAnalysis.lib.distances.transform_RtoS"><tt class="xref py py-meth docutils literal"><span class="pre">transform_RtoS()</span></tt></a></p>
+<p>Reciprocal operation to <a class="reference internal" href="#MDAnalysis.lib.distances.transform_RtoS" title="MDAnalysis.lib.distances.transform_RtoS"><code class="xref py py-meth docutils literal"><span class="pre">transform_RtoS()</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>inputcoords</em></dt>
 <dd><p class="first last">An n x 3 array of coordinate data, of type np.float32</p>
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">The unitcell dimesions for this system
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>outcoords</em></dt>
 <dd><p class="first last">An n x 3 array of fracional coordiantes</p>
 </dd>
@@ -500,27 +511,27 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">applyPBC</tt><big>(</big><em>incoords</em>, <em>box</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#applyPBC"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">apply_PBC</code><span class="sig-paren">(</span><em>incoords</em>, <em>box</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#apply_PBC"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Moves a set of coordinates to all be within the primary unit cell</p>
-<p>newcoords = applyPBC(coords, box)</p>
+<p>newcoords = apply_PBC(coords, box)</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>coords</em></dt>
 <dd><p class="first last">coordinate array (of type numpy.float32)</p>
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">box dimensions, can be either orthogonal or triclinic information
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>newcoords</em></dt>
 <dd><p class="first last">coordinates that are now all within the primary unit cell,
 as defined by box</p>
@@ -530,20 +541,21 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">calc_angles</tt><big>(</big><em>coords1</em>, <em>coords2</em>, <em>coords3</em>, <em>box=None</em>, <em>result=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_angles"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">calc_angles</code><span class="sig-paren">(</span><em>coords1</em>, <em>coords2</em>, <em>coords3</em>, <em>box=None</em>, <em>result=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_angles"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Calculates the angle formed between three atoms, over a list of coordinates.
 All <em>atom</em> inputs are lists of coordinates of equal length, with <em>atom2</em>
 representing the apex of the angle.</p>
-<p>If a 1D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with <tt class="docutils literal"><span class="pre">len(atom1)</span></tt> elements is
+<p>If a 1D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with <code class="docutils literal"><span class="pre">len(atom1)</span></code> elements is
 provided in <em>result</em> then this preallocated array is filled. This can speed
 up calculations.</p>
-<p>The optional argument <tt class="docutils literal"><span class="pre">box</span></tt> ensures that periodic boundaries are taken into account when
+<p>The optional argument <code class="docutils literal"><span class="pre">box</span></code> ensures that periodic boundaries are taken into account when
 constructing the connecting vectors between atoms, ie that the vector between atoms 1 &amp; 2
 goes between coordinates in the same image.</p>
 <p>angles = calc_angles(coords1, coords2, coords3, [[box=None],result=angles])</p>
@@ -551,7 +563,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>coords1</em></dt>
 <dd><p class="first last">coordinate array of one side of angles</p>
 </dd>
@@ -566,7 +578,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 atoms respect minimum image convention.  This is import when the angle might
 be between atoms in different images.
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
@@ -576,7 +588,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>angles</em></dt>
 <dd><p class="first last">A numpy.array of angles in radians</p>
 </dd>
@@ -585,25 +597,28 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Added optional box argument to account for periodic boundaries in calculation</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Added optional box argument to account for periodic boundaries in calculation</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">calc_bonds</tt><big>(</big><em>coords1</em>, <em>coords2</em>, <em>box=None</em>, <em>result=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_bonds"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">calc_bonds</code><span class="sig-paren">(</span><em>coords1</em>, <em>coords2</em>, <em>box=None</em>, <em>result=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_bonds"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Calculate all distances between a pair of atoms.  <em>atom1</em> and <em>atom2</em> are both
 arrays of coordinates, where atom1[i] and atom2[i] represent a bond.</p>
 <p>In comparison to distance_array and self_distance_array which calculate distances
 between all combinations of coordinates, calc_bonds can be used to calculate distance
 between pairs of objects, similar to:</p>
-<div class="highlight-python"><pre>numpy.linalg.norm(a - b) for a, b in zip(coords1, coords2)</pre>
+<div class="highlight-python"><div class="highlight"><pre>numpy.linalg.norm(a - b) for a, b in zip(coords1, coords2)
+</pre></div>
 </div>
 <p>The optional argument <em>box</em> applies minimum image convention if supplied.
 <em>box</em> can be either orthogonal or triclinic</p>
-<p>If a 1D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with <tt class="docutils literal"><span class="pre">len(atom1)</span></tt> elements is
+<p>If a 1D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with <code class="docutils literal"><span class="pre">len(atom1)</span></code> elements is
 provided in <em>result</em> then this preallocated array is filled. This can speed
 up calculations.</p>
 <p>bondlengths = calc_bonds(coords1, coords2 [, box [,result=bondlengths]])</p>
@@ -611,7 +626,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>coords1</em></dt>
 <dd><p class="first last">An array of coordinates for one half of the bond</p>
 </dd>
@@ -621,7 +636,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 <dt><em>box</em></dt>
 <dd><p class="first last">Unit cell information if periodic boundary conditions are required [None]
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
@@ -632,7 +647,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>bondlengths</em></dt>
 <dd><p class="first last">Numpy array with the length between each pair in coords1 and coords2</p>
 </dd>
@@ -641,26 +656,28 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">calc_dihedrals</tt><big>(</big><em>coords1</em>, <em>coords2</em>, <em>coords3</em>, <em>coords4</em>, <em>box=None</em>, <em>result=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_dihedrals"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">calc_dihedrals</code><span class="sig-paren">(</span><em>coords1</em>, <em>coords2</em>, <em>coords3</em>, <em>coords4</em>, <em>box=None</em>, <em>result=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#calc_dihedrals"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Calculate the dihedral angle formed by four atoms, over a list of coordinates.</p>
 <p>Dihedral angle around axis connecting atoms 1 and 2 (i.e. the angle
 between the planes spanned by atoms (0,1,2) and (1,2,3)):</p>
-<div class="highlight-python"><pre>        3
+<div class="highlight-python"><div class="highlight"><pre>        3
         |
   1-----2
  /
-0</pre>
+0
+</pre></div>
 </div>
-<p>If a 1D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with <tt class="docutils literal"><span class="pre">len(atom1)</span></tt> elements is
+<p>If a 1D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with <code class="docutils literal"><span class="pre">len(atom1)</span></code> elements is
 provided in <em>result</em> then this preallocated array is filled. This can speed
 up calculations.</p>
-<p>The optional argument <tt class="docutils literal"><span class="pre">box</span></tt> ensures that periodic boundaries are taken into
+<p>The optional argument <code class="docutils literal"><span class="pre">box</span></code> ensures that periodic boundaries are taken into
 account when constructing the connecting vectors between atoms, ie that the vector
 between atoms 1 &amp; 2 goes between coordinates in the same image.</p>
 <p>angles = calc_dihedrals(coords1, coords2, coords3, coords4 [,box=box, result=angles])</p>
@@ -668,7 +685,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>coords1</em></dt>
 <dd><p class="first last">coordinate array of 1st atom in dihedrals</p>
 </dd>
@@ -686,7 +703,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 between atoms respect minimum image convention.  This is import when the
 angle might be between atoms in different images.
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
@@ -696,7 +713,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>angles</em></dt>
 <dd><p class="first last">A numpy.array of angles in radians</p>
 </dd>
@@ -705,29 +722,34 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Added optional box argument to account for periodic boundaries in calculation</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Added optional box argument to account for periodic boundaries in calculation</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Renamed from calc_torsions to calc_dihedrals</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">distance_array</tt><big>(</big><em>reference</em>, <em>configuration</em>, <em>box=None</em>, <em>result=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#distance_array"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">distance_array</code><span class="sig-paren">(</span><em>reference</em>, <em>configuration</em>, <em>box=None</em>, <em>result=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#distance_array"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Calculate all distances between a reference set and another configuration.</p>
 <p>If there are <em>i</em> positions in reference, and <em>j</em> positions in configuration,
 will calculate a <em>i</em> x <em>j</em> array of distances
 If an <em>box</em> is supplied then a minimum image convention is used when
 calculating distances.</p>
-<p>If a 2D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with the shape <tt class="docutils literal"><span class="pre">(len(reference),</span>
-<span class="pre">len(configuration))</span></tt> is provided in <em>result</em> then this preallocated array is
+<p>If a 2D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with the shape <code class="docutils literal"><span class="pre">(len(reference),</span>
+<span class="pre">len(configuration))</span></code> is provided in <em>result</em> then this preallocated array is
 filled. This can speed up calculations.</p>
 <p>d = distance_array(reference, configuration[,box[,result=d]])</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>reference</em></dt>
 <dd><p class="first last">reference coordinate array (must be numpy.float32)</p>
 </dd>
@@ -736,21 +758,21 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">cell dimensions (minimum image convention is applied)
-or None [<tt class="docutils literal"><span class="pre">None</span></tt>].
+or None [<code class="docutils literal"><span class="pre">None</span></code>].
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
 <dd><p class="first last">optional preallocated result array which must have the
 shape (len(ref), len(conf)) and dtype=numpy.float64.
 Avoids creating the array which saves time when the function
-is called repeatedly. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+is called repeatedly. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>d</em></dt>
 <dd><p class="first last">(len(reference),len(configuration)) numpy array with the distances d[i,j]
 between reference coordinates i and configuration coordinates j</p>
@@ -769,38 +791,38 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">self_distance_array</tt><big>(</big><em>reference</em>, <em>box=None</em>, <em>result=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#self_distance_array"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">self_distance_array</code><span class="sig-paren">(</span><em>reference</em>, <em>box=None</em>, <em>result=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#self_distance_array"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Calculate all distances within a configuration <em>reference</em>.</p>
 <p>If a <em>box</em> is supplied then a minimum image convention is used before
 calculating distances.</p>
-<p>If a 1D numpy array of dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt> with the shape
-<tt class="docutils literal"><span class="pre">(N*(N-1)/2)</span></tt> is provided in <em>result</em> then this preallocated array
+<p>If a 1D numpy array of dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code> with the shape
+<code class="docutils literal"><span class="pre">(N*(N-1)/2)</span></code> is provided in <em>result</em> then this preallocated array
 is filled. This can speed up calculations.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>ref</em></dt>
 <dd><p class="first last">reference coordinate array with N=len(ref) coordinates</p>
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">cell dimensions (minimum image convention is applied)
-or None [<tt class="docutils literal"><span class="pre">None</span></tt>]
+or None [<code class="docutils literal"><span class="pre">None</span></code>]
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 <dt><em>result</em></dt>
 <dd><p class="first last">optional preallocated result array which must have the shape
-(N*(N-1)/2,) and dtype <tt class="docutils literal"><span class="pre">numpy.float64</span></tt>. Avoids creating
+(N*(N-1)/2,) and dtype <code class="docutils literal"><span class="pre">numpy.float64</span></code>. Avoids creating
 the array which saves time when the function is called
-repeatedly. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+repeatedly. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>d</em></dt>
 <dd><p class="first">N*(N-1)/2 numpy 1D array with the distances dist[i,j] between ref
 coordinates i and j at position d[k]. Loop through d:</p>
@@ -825,28 +847,28 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">transform_RtoS</tt><big>(</big><em>inputcoords</em>, <em>box</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#transform_RtoS"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">transform_RtoS</code><span class="sig-paren">(</span><em>inputcoords</em>, <em>box</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#transform_RtoS"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Transform an array of coordinates from real space to S space (aka lambda space)</p>
 <p>S space represents fractional space within the unit cell for this system</p>
-<p>Reciprocal operation to <a class="reference internal" href="#MDAnalysis.lib.distances.transform_StoR" title="MDAnalysis.lib.distances.transform_StoR"><tt class="xref py py-meth docutils literal"><span class="pre">transform_StoR()</span></tt></a></p>
+<p>Reciprocal operation to <a class="reference internal" href="#MDAnalysis.lib.distances.transform_StoR" title="MDAnalysis.lib.distances.transform_StoR"><code class="xref py py-meth docutils literal"><span class="pre">transform_StoR()</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>inputcoords</em></dt>
 <dd><p class="first last">An n x 3 array of coordinate data, of type np.float32</p>
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">The unitcell dimesions for this system
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>outcoords</em></dt>
 <dd><p class="first last">An n x 3 array of fractional coordiantes</p>
 </dd>
@@ -859,28 +881,28 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.distances.</tt><tt class="descname">transform_StoR</tt><big>(</big><em>inputcoords</em>, <em>box</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#transform_StoR"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.distances.</code><code class="descname">transform_StoR</code><span class="sig-paren">(</span><em>inputcoords</em>, <em>box</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/distances.html#transform_StoR"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Transform an array of coordinates from S space into real space.</p>
 <p>S space represents fractional space within the unit cell for this system</p>
-<p>Reciprocal operation to <a class="reference internal" href="#MDAnalysis.lib.distances.transform_RtoS" title="MDAnalysis.lib.distances.transform_RtoS"><tt class="xref py py-meth docutils literal"><span class="pre">transform_RtoS()</span></tt></a></p>
+<p>Reciprocal operation to <a class="reference internal" href="#MDAnalysis.lib.distances.transform_RtoS" title="MDAnalysis.lib.distances.transform_RtoS"><code class="xref py py-meth docutils literal"><span class="pre">transform_RtoS()</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>inputcoords</em></dt>
 <dd><p class="first last">An n x 3 array of coordinate data, of type np.float32</p>
 </dd>
 <dt><em>box</em></dt>
 <dd><p class="first last">The unitcell dimesions for this system
 Cell dimensions must be in an identical to format to those returned
-by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></tt></a>,
+by <a class="reference internal" href="../coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions" title="MDAnalysis.coordinates.base.Timestep.dimensions"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.coordinates.base.Timestep.dimensions</span></code></a>,
 [lx, ly, lz, alpha, beta, gamma]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>outcoords</em></dt>
 <dd><p class="first last">An n x 3 array of fracional coordiantes</p>
 </dd>
@@ -900,7 +922,7 @@ <h2>9.1.1. Functions<a class="headerlink" href="#functions" title="Permalink to
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -915,11 +937,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../lib_modules.html" title="9. MDAnalysis library"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -929,7 +951,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/lib/log.html b/package/doc/html/documentation_pages/lib/log.html
index fcb89d74aec..c9208d9737a 100644
--- a/package/doc/html/documentation_pages/lib/log.html
+++ b/package/doc/html/documentation_pages/lib/log.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>9.4. Setting up logging — MDAnalysis.lib.log &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>9.4. Setting up logging — MDAnalysis.lib.log &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="9. MDAnalysis library" href="../lib_modules.html" />
     <link rel="next" title="9.5. Mathematical helper functions — MDAnalysis.lib.mdamath" href="mdamath.html" />
-    <link rel="prev" title="9.3.2. Fast atom neighbor lookup using a KD tree (implemented in C++) — MDAnalysis.lib.KDTree.NeighborSearch" href="KDTree/NeighborSearch.html" /> 
+    <link rel="prev" title="9.3. Neighbor Search wrapper for MDAnalysis — :mod: MDAnalysis.lib.NeighborSearch" href="NeighborSearch.html" /> 
   </head>
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+    <div class="related" role="navigation" aria-label="related navigation">
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@@ -49,20 +47,20 @@ <h3>Navigation</h3>
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              accesskey="N">next</a> |</li>
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-          <a href="KDTree/NeighborSearch.html" title="9.3.2. Fast atom neighbor lookup using a KD tree (implemented in C++) — MDAnalysis.lib.KDTree.NeighborSearch"
+          <a href="NeighborSearch.html" title="9.3. Neighbor Search wrapper for MDAnalysis — :mod: MDAnalysis.lib.NeighborSearch"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
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   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">9.4. Setting up logging &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.log</span></tt></a><ul>
+<li><a class="reference internal" href="#">9.4. Setting up logging &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.log</span></code></a><ul>
 <li><a class="reference internal" href="#convenience-functions">9.4.1. Convenience functions</a></li>
 <li><a class="reference internal" href="#other-functions-and-classes-for-logging-purposes">9.4.2. Other functions and classes for logging purposes</a></li>
 </ul>
@@ -70,17 +68,19 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 </ul>
 
   <h4>Previous topic</h4>
-  <p class="topless"><a href="KDTree/NeighborSearch.html"
-                        title="previous chapter">9.3.2. Fast atom neighbor lookup using a KD tree (implemented in C++) &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.lib.KDTree.NeighborSearch</span></tt></a></p>
+  <p class="topless"><a href="NeighborSearch.html"
+                        title="previous chapter">9.3. Neighbor Search wrapper for MDAnalysis &#8212; :mod: <cite>MDAnalysis.lib.NeighborSearch</cite></a></p>
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+                        title="next chapter">9.5. Mathematical helper functions &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.mdamath</span></code></a></p>
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   <span class="target" id="module-MDAnalysis.lib.log"></span><div class="section" id="setting-up-logging-mdanalysis-lib-log">
-<h1>9.4. Setting up logging &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.log" title="MDAnalysis.lib.log"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.log</span></tt></a><a class="headerlink" href="#setting-up-logging-mdanalysis-lib-log" title="Permalink to this headline">¶</a></h1>
+<h1>9.4. Setting up logging &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.log" title="MDAnalysis.lib.log"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.log</span></code></a><a class="headerlink" href="#setting-up-logging-mdanalysis-lib-log" title="Permalink to this headline">¶</a></h1>
 <p>Configure logging for MDAnalysis. Import this module if logging is
 desired in application code.</p>
 <p>Logging to a file and the console is set up by default as described
 under <a class="reference external" href="http://docs.python.org/library/logging.html?#logging-to-multiple-destinations">logging to multiple destinations</a>.</p>
 <p>The top level logger of the library is named <em>MDAnalysis</em> by
 convention; a simple logger that writes to the console and logfile can
-be created with the <a class="reference internal" href="#MDAnalysis.lib.log.create" title="MDAnalysis.lib.log.create"><tt class="xref py py-func docutils literal"><span class="pre">create()</span></tt></a> function. This only has to be done
+be created with the <a class="reference internal" href="#MDAnalysis.lib.log.create" title="MDAnalysis.lib.log.create"><code class="xref py py-func docutils literal"><span class="pre">create()</span></code></a> function. This only has to be done
 <em>once</em>. For convenience, the default MDAnalysis logger can be created
-with <a class="reference internal" href="#MDAnalysis.start_logging" title="MDAnalysis.start_logging"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.start_logging()</span></tt></a>:</p>
+with <a class="reference internal" href="#MDAnalysis.start_logging" title="MDAnalysis.start_logging"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.start_logging()</span></code></a>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">MDAnalysis</span>
 <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">start_logging</span><span class="p">()</span>
 </pre></div>
 </div>
 <p>Once this has been done, MDAnalysis will write messages to the logfile
 (named <cite>MDAnalysis.log</cite> by default but this can be changed with the
-optional argument to <a class="reference internal" href="#MDAnalysis.start_logging" title="MDAnalysis.start_logging"><tt class="xref py py-func docutils literal"><span class="pre">start_logging()</span></tt></a>).</p>
+optional argument to <a class="reference internal" href="#MDAnalysis.start_logging" title="MDAnalysis.start_logging"><code class="xref py py-func docutils literal"><span class="pre">start_logging()</span></code></a>).</p>
 <p>Any code can log to the MDAnalysis logger by using</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">logging</span>
 <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s">&#39;MDAnalysis.MODULENAME&#39;</span><span class="p">)</span>
@@ -129,9 +129,9 @@ <h1>9.4. Setting up logging &#8212; <a class="reference internal" href="#module-
 </div>
 <p>The important point is that the name of the logger begins with
 &#8220;MDAnalysis.&#8221;.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last">The <a class="reference external" href="http://docs.python.org/library/logging.html#module-logging" title="(in Python v2.7)"><tt class="xref py py-mod docutils literal"><span class="pre">logging</span></tt></a> module in the standard library contains
+<p class="last">The <a class="reference external" href="http://docs.python.org/library/logging.html#module-logging" title="(in Python v2.7)"><code class="xref py py-mod docutils literal"><span class="pre">logging</span></code></a> module in the standard library contains
 in depth documentation about using logging.</p>
 </div>
 <div class="section" id="convenience-functions">
@@ -140,7 +140,7 @@ <h2>9.4.1. Convenience functions<a class="headerlink" href="#convenience-functio
 stop the default <em>MDAnalysis</em> logger.</p>
 <dl class="function">
 <dt id="MDAnalysis.start_logging">
-<tt class="descclassname">MDAnalysis.</tt><tt class="descname">start_logging</tt><big>(</big><em>logfile='MDAnalysis.log'</em>, <em>version='0.11.0-dev'</em><big>)</big><a class="headerlink" href="#MDAnalysis.start_logging" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.</code><code class="descname">start_logging</code><span class="sig-paren">(</span><em>logfile='MDAnalysis.log'</em>, <em>version='0.11.0'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#start_logging"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.start_logging" title="Permalink to this definition">¶</a></dt>
 <dd><p>Start logging of messages to file and console.</p>
 <p>The default logfile is named <cite>MDAnalysis.log</cite> and messages are
 logged with the tag <em>MDAnalysis</em>.</p>
@@ -148,7 +148,7 @@ <h2>9.4.1. Convenience functions<a class="headerlink" href="#convenience-functio
 
 <dl class="function">
 <dt id="MDAnalysis.stop_logging">
-<tt class="descclassname">MDAnalysis.</tt><tt class="descname">stop_logging</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.stop_logging" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.</code><code class="descname">stop_logging</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#stop_logging"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.stop_logging" title="Permalink to this definition">¶</a></dt>
 <dd><p>Stop logging to logfile and console.</p>
 </dd></dl>
 
@@ -157,7 +157,7 @@ <h2>9.4.1. Convenience functions<a class="headerlink" href="#convenience-functio
 <h2>9.4.2. Other functions and classes for logging purposes<a class="headerlink" href="#other-functions-and-classes-for-logging-purposes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.lib.log.NullHandler">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.lib.log.</tt><tt class="descname">NullHandler</tt><big>(</big><em>level=0</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#NullHandler"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.NullHandler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.lib.log.</code><code class="descname">NullHandler</code><span class="sig-paren">(</span><em>level=0</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#NullHandler"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.NullHandler" title="Permalink to this definition">¶</a></dt>
 <dd><p>Silent Handler.</p>
 <p>Useful as a default:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">h</span> <span class="o">=</span> <span class="n">NullHandler</span><span class="p">()</span>
@@ -173,7 +173,7 @@ <h2>9.4.2. Other functions and classes for logging purposes<a class="headerlink"
 
 <dl class="class">
 <dt id="MDAnalysis.lib.log.ProgressMeter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.lib.log.</tt><tt class="descname">ProgressMeter</tt><big>(</big><em>numsteps</em>, <em>format=None</em>, <em>interval=10</em>, <em>offset=0</em>, <em>quiet=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#ProgressMeter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.ProgressMeter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.lib.log.</code><code class="descname">ProgressMeter</code><span class="sig-paren">(</span><em>numsteps</em>, <em>format=None</em>, <em>interval=10</em>, <em>offset=0</em>, <em>quiet=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#ProgressMeter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.ProgressMeter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Simple progress meter</p>
 <p>Usage:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">u</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span> <span class="n">DCD</span><span class="p">)</span>
@@ -185,15 +185,16 @@ <h2>9.4.2. Other functions and classes for logging purposes<a class="headerlink"
 </div>
 <p>For a trajectory with 10000 frames this will produce output such
 as</p>
-<div class="highlight-python"><pre>Step   100/10000 [  1.0%]
+<div class="highlight-python"><div class="highlight"><pre>Step   100/10000 [  1.0%]
 Step   200/10000 [  2.0%]
-...</pre>
+...
+</pre></div>
 </div>
 <p>Because the default <em>format</em> string</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="s">&quot;Step </span><span class="si">%(step)5d</span><span class="s">/</span><span class="si">%(numsteps)d</span><span class="s"> [</span><span class="si">%(percentage)5.1f%%</span><span class="s">]</span><span class="se">\r</span><span class="s">&quot;</span>
 </pre></div>
 </div>
-<p>ends with a carriage return <tt class="docutils literal"><span class="pre">\r</span></tt> and not a newline <tt class="docutils literal"><span class="pre">\n</span></tt>, the
+<p>ends with a carriage return <code class="docutils literal"><span class="pre">\r</span></code> and not a newline <code class="docutils literal"><span class="pre">\n</span></code>, the
 lines will be printed on top of each other.</p>
 <p>It is possible to embed (almost) arbitrary additional data in the
 format string, for example a current RMSD value:</p>
@@ -217,14 +218,14 @@ <h2>9.4.2. Other functions and classes for logging purposes<a class="headerlink"
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>numsteps</em></dt>
 <dd><p class="first last">total number of steps</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>interval</em></dt>
 <dd><p class="first last">only calculate progress every <em>interval</em> steps [10]</p>
 </dd>
@@ -238,10 +239,10 @@ <h2>9.4.2. Other functions and classes for logging purposes<a class="headerlink"
 <li><em>percentage</em>: percentage of total</li>
 </ul>
 </div></blockquote>
-<p>The last call to <tt class="xref py py-meth docutils literal"><span class="pre">ProgressMeter.print()</span></tt> will automatically
-issue a newline <tt class="docutils literal"><span class="pre">\n</span></tt> if the last character is the carriage
-return <tt class="docutils literal"><span class="pre">\r</span></tt>.</p>
-<p class="last">If <em>format</em> is <tt class="docutils literal"><span class="pre">None</span></tt> then the default is used.
+<p>The last call to <code class="xref py py-meth docutils literal"><span class="pre">ProgressMeter.print()</span></code> will automatically
+issue a newline <code class="docutils literal"><span class="pre">\n</span></code> if the last character is the carriage
+return <code class="docutils literal"><span class="pre">\r</span></code>.</p>
+<p class="last">If <em>format</em> is <code class="docutils literal"><span class="pre">None</span></code> then the default is used.
 [&#8220;Step %(step)5d/%(numsteps)d [%(percentage)5.1f%%]r&#8221;]</p>
 </dd>
 <dt><em>offset</em></dt>
@@ -249,24 +250,25 @@ <h2>9.4.2. Other functions and classes for logging purposes<a class="headerlink"
 set <em>offset</em> = 1 [0]</p>
 </dd>
 <dt><em>quiet</em></dt>
-<dd><p class="first last">If <tt class="docutils literal"><span class="pre">True</span></tt>, disable all output, <tt class="docutils literal"><span class="pre">False</span></tt> print all messages as
-specified, [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">If <code class="docutils literal"><span class="pre">True</span></code>, disable all output, <code class="docutils literal"><span class="pre">False</span></code> print all messages as
+specified, [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.8: </span>Keyword argument <em>quiet</em> was added.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.8: </span>Keyword argument <em>quiet</em> was added.</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.lib.log.ProgressMeter.echo">
-<tt class="descname">echo</tt><big>(</big><em>step</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#ProgressMeter.echo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.ProgressMeter.echo" title="Permalink to this definition">¶</a></dt>
+<code class="descname">echo</code><span class="sig-paren">(</span><em>step</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#ProgressMeter.echo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.ProgressMeter.echo" title="Permalink to this definition">¶</a></dt>
 <dd><p>Print the state to stderr, but only every <em>interval</em> steps.</p>
 <ol class="arabic simple">
-<li>calls <a class="reference internal" href="#MDAnalysis.lib.log.ProgressMeter.update" title="MDAnalysis.lib.log.ProgressMeter.update"><tt class="xref py py-meth docutils literal"><span class="pre">update()</span></tt></a></li>
-<li>writes step and percentage to stderr with <a class="reference internal" href="#MDAnalysis.lib.log.echo" title="MDAnalysis.lib.log.echo"><tt class="xref py py-func docutils literal"><span class="pre">echo()</span></tt></a>,
-using the format string (in <tt class="xref py py-attr docutils literal"><span class="pre">ProgressMeter.format</span></tt>)</li>
+<li>calls <a class="reference internal" href="#MDAnalysis.lib.log.ProgressMeter.update" title="MDAnalysis.lib.log.ProgressMeter.update"><code class="xref py py-meth docutils literal"><span class="pre">update()</span></code></a></li>
+<li>writes step and percentage to stderr with <a class="reference internal" href="#MDAnalysis.lib.log.echo" title="MDAnalysis.lib.log.echo"><code class="xref py py-func docutils literal"><span class="pre">echo()</span></code></a>,
+using the format string (in <code class="xref py py-attr docutils literal"><span class="pre">ProgressMeter.format</span></code>)</li>
 </ol>
 <p>The last step is always shown, even if not on an <em>interval</em>, and a
 carriage return is replaced with a new line for a cleaner display.</p>
@@ -274,16 +276,16 @@ <h2>9.4.2. Other functions and classes for logging purposes<a class="headerlink"
 the format string.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">If <em>quiet</em> = <tt class="docutils literal"><span class="pre">True</span></tt> has been set in the
-constructor or if <tt class="xref py py-attr docutils literal"><span class="pre">ProgressMeter.quiet</span></tt> has
-been set to <tt class="docutils literal"><span class="pre">True</span></tt> the no messages will be
+<p class="last">If <em>quiet</em> = <code class="docutils literal"><span class="pre">True</span></code> has been set in the
+constructor or if <code class="xref py py-attr docutils literal"><span class="pre">ProgressMeter.quiet</span></code> has
+been set to <code class="docutils literal"><span class="pre">True</span></code> the no messages will be
 printed.</p>
 </div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.log.ProgressMeter.update">
-<tt class="descname">update</tt><big>(</big><em>step</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#ProgressMeter.update"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.ProgressMeter.update" title="Permalink to this definition">¶</a></dt>
+<code class="descname">update</code><span class="sig-paren">(</span><em>step</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#ProgressMeter.update"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.ProgressMeter.update" title="Permalink to this definition">¶</a></dt>
 <dd><p>Update the state of the ProgressMeter.</p>
 <p><em>kwargs</em> are additional attributes that can be references in
 the format string.</p>
@@ -293,14 +295,14 @@ <h2>9.4.2. Other functions and classes for logging purposes<a class="headerlink"
 
 <dl class="function">
 <dt id="MDAnalysis.lib.log.clear_handlers">
-<tt class="descclassname">MDAnalysis.lib.log.</tt><tt class="descname">clear_handlers</tt><big>(</big><em>logger</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#clear_handlers"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.clear_handlers" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.log.</code><code class="descname">clear_handlers</code><span class="sig-paren">(</span><em>logger</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#clear_handlers"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.clear_handlers" title="Permalink to this definition">¶</a></dt>
 <dd><p>clean out handlers in the library top level logger</p>
 <p>(only important for reload/debug cycles...)</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.log.create">
-<tt class="descclassname">MDAnalysis.lib.log.</tt><tt class="descname">create</tt><big>(</big><em>logger_name='MDAnalysis'</em>, <em>logfile='MDAnalysis.log'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.create" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.log.</code><code class="descname">create</code><span class="sig-paren">(</span><em>logger_name='MDAnalysis'</em>, <em>logfile='MDAnalysis.log'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.create" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a top level logger.</p>
 <ul class="simple">
 <li>The file logger logs everything (including DEBUG).</li>
@@ -316,13 +318,13 @@ <h2>9.4.2. Other functions and classes for logging purposes<a class="headerlink"
 
 <dl class="function">
 <dt id="MDAnalysis.lib.log.echo">
-<tt class="descclassname">MDAnalysis.lib.log.</tt><tt class="descname">echo</tt><big>(</big><em>s=''</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#echo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.echo" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.log.</code><code class="descname">echo</code><span class="sig-paren">(</span><em>s=''</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#echo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.echo" title="Permalink to this definition">¶</a></dt>
 <dd><p>Simple string output that immediately prints to the console.</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.log.start_logging">
-<tt class="descclassname">MDAnalysis.lib.log.</tt><tt class="descname">start_logging</tt><big>(</big><em>logfile='MDAnalysis.log'</em>, <em>version='0.11.0-dev'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#start_logging"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.start_logging" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.log.</code><code class="descname">start_logging</code><span class="sig-paren">(</span><em>logfile='MDAnalysis.log'</em>, <em>version='0.11.0'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#start_logging"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.start_logging" title="Permalink to this definition">¶</a></dt>
 <dd><p>Start logging of messages to file and console.</p>
 <p>The default logfile is named <cite>MDAnalysis.log</cite> and messages are
 logged with the tag <em>MDAnalysis</em>.</p>
@@ -330,7 +332,7 @@ <h2>9.4.2. Other functions and classes for logging purposes<a class="headerlink"
 
 <dl class="function">
 <dt id="MDAnalysis.lib.log.stop_logging">
-<tt class="descclassname">MDAnalysis.lib.log.</tt><tt class="descname">stop_logging</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#stop_logging"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.stop_logging" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.log.</code><code class="descname">stop_logging</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/log.html#stop_logging"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.log.stop_logging" title="Permalink to this definition">¶</a></dt>
 <dd><p>Stop logging to logfile and console.</p>
 </dd></dl>
 
@@ -343,7 +345,7 @@ <h2>9.4.2. Other functions and classes for logging purposes<a class="headerlink"
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -356,13 +358,13 @@ <h3>Navigation</h3>
           <a href="mdamath.html" title="9.5. Mathematical helper functions — MDAnalysis.lib.mdamath"
              >next</a> |</li>
         <li class="right" >
-          <a href="KDTree/NeighborSearch.html" title="9.3.2. Fast atom neighbor lookup using a KD tree (implemented in C++) — MDAnalysis.lib.KDTree.NeighborSearch"
+          <a href="NeighborSearch.html" title="9.3. Neighbor Search wrapper for MDAnalysis — :mod: MDAnalysis.lib.NeighborSearch"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -372,7 +374,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/lib/mdamath.html b/package/doc/html/documentation_pages/lib/mdamath.html
index 9ef2c44a71b..cc5d7b41aaa 100644
--- a/package/doc/html/documentation_pages/lib/mdamath.html
+++ b/package/doc/html/documentation_pages/lib/mdamath.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>9.5. Mathematical helper functions — MDAnalysis.lib.mdamath &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>9.5. Mathematical helper functions — MDAnalysis.lib.mdamath &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
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       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
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     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="9. MDAnalysis library" href="../lib_modules.html" />
     <link rel="next" title="9.6. Parallel algorithms for MDAnalysis" href="parallel.html" />
     <link rel="prev" title="9.4. Setting up logging — MDAnalysis.lib.log" href="log.html" /> 
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+    <div class="related" role="navigation" aria-label="related navigation">
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              accesskey="P">previous</a> |</li>
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-          <li><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
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+                        title="previous chapter">9.4. Setting up logging &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.log</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="parallel.html"
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-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/lib/mdamath.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
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   <span class="target" id="module-MDAnalysis.lib.mdamath"></span><div class="section" id="mathematical-helper-functions-mdanalysis-lib-mdamath">
-<h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.mdamath" title="MDAnalysis.lib.mdamath"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.mdamath</span></tt></a><a class="headerlink" href="#mathematical-helper-functions-mdanalysis-lib-mdamath" title="Permalink to this headline">¶</a></h1>
+<h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.mdamath" title="MDAnalysis.lib.mdamath"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.mdamath</span></code></a><a class="headerlink" href="#mathematical-helper-functions-mdanalysis-lib-mdamath" title="Permalink to this headline">¶</a></h1>
 <p>Helper functions for common mathematical operations</p>
 <dl class="function">
 <dt id="MDAnalysis.lib.mdamath.normal">
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">normal</tt><big>(</big><em>vec1</em>, <em>vec2</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#normal"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.normal" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">normal</code><span class="sig-paren">(</span><em>vec1</em>, <em>vec2</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#normal"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.normal" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns the unit vector normal to two vectors.</p>
 <div class="math">
 \[\hat{\mathbf{n}} = \frac{\mathbf{v}_1 \times \mathbf{v}_2}{|\mathbf{v}_1 \times \mathbf{v}_2|}\]</div>
 <p>If the two vectors are collinear, the vector <span class="math">\(\mathbf{0}\)</span> is returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.mdamath.norm">
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">norm</tt><big>(</big><em>v</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#norm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.norm" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns the length of a vector, <tt class="docutils literal"><span class="pre">sqrt(v.v)</span></tt>.</p>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">norm</code><span class="sig-paren">(</span><em>v</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#norm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.norm" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the length of a vector, <code class="docutils literal"><span class="pre">sqrt(v.v)</span></code>.</p>
 <div class="math">
 \[v = \sqrt{\mathbf{v}\cdot\mathbf{v}}\]</div>
-<p>Faster than <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.norm.html#numpy.linalg.norm" title="(in NumPy v1.9)"><tt class="xref py py-func docutils literal"><span class="pre">numpy.linalg.norm()</span></tt></a> because no frills.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+<p>Faster than <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.norm.html#numpy.linalg.norm" title="(in NumPy v1.9)"><code class="xref py py-func docutils literal"><span class="pre">numpy.linalg.norm()</span></code></a> because no frills.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.mdamath.angle">
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">angle</tt><big>(</big><em>a</em>, <em>b</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#angle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.angle" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">angle</code><span class="sig-paren">(</span><em>a</em>, <em>b</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#angle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.angle" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns the angle between two vectors in radians</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.mdamath.dihedral">
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">dihedral</tt><big>(</big><em>ab</em>, <em>bc</em>, <em>cd</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#dihedral"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.dihedral" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">dihedral</code><span class="sig-paren">(</span><em>ab</em>, <em>bc</em>, <em>cd</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#dihedral"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.dihedral" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns the dihedral angle in radians between vectors connecting A,B,C,D.</p>
 <p>The dihedral measures the rotation around bc:</p>
-<div class="highlight-python"><pre>  ab
+<div class="highlight-python"><div class="highlight"><pre>  ab
 A----&gt;B
        \ bc
-       _\'
+       _\&#39;
          C----&gt;D
-           cd</pre>
+           cd
+</pre></div>
 </div>
 <p>The dihedral angle is restricted to the range -π &lt;= x &lt;= π.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.mdamath.stp">
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">stp</tt><big>(</big><em>vec1</em>, <em>vec2</em>, <em>vec3</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#stp"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.stp" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">stp</code><span class="sig-paren">(</span><em>vec1</em>, <em>vec2</em>, <em>vec3</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#stp"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.stp" title="Permalink to this definition">¶</a></dt>
 <dd><p>Takes the scalar triple product of three vectors.</p>
 <p>Returns the volume <em>V</em> of the parallel epiped spanned by the three
 vectors</p>
 <div class="math">
 \[V = \mathbf{v}_3 \cdot (\mathbf{v}_1 \times \mathbf{v}_2)\]</div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.mdamath.triclinic_box">
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">triclinic_box</tt><big>(</big><em>x</em>, <em>y</em>, <em>z</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#triclinic_box"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.triclinic_box" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">triclinic_box</code><span class="sig-paren">(</span><em>x</em>, <em>y</em>, <em>z</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#triclinic_box"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.triclinic_box" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert the three triclinic box vectors to [A,B,C,alpha,beta,gamma].</p>
 <p>Angles are in degrees.</p>
 <ul class="simple">
@@ -166,7 +173,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 <li>beta   = angle(x,z)</li>
 <li>gamma  = angle(x,y)</li>
 </ul>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">Definition of angles: <a class="reference external" href="http://en.wikipedia.org/wiki/Lattice_constant">http://en.wikipedia.org/wiki/Lattice_constant</a></p>
 </div>
@@ -174,7 +181,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 
 <dl class="function">
 <dt id="MDAnalysis.lib.mdamath.triclinic_vectors">
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">triclinic_vectors</tt><big>(</big><em>dimensions</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#triclinic_vectors"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.triclinic_vectors" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">triclinic_vectors</code><span class="sig-paren">(</span><em>dimensions</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#triclinic_vectors"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.triclinic_vectors" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert <cite>[A,B,C,alpha,beta,gamma]</cite> to a triclinic box representation.</p>
 <p>Original <a class="reference external" href="http://www.mail-archive.com/gmx-users&#64;gromacs.org/msg28032.html">code by Tsjerk Wassenaar</a> posted on the Gromacs mailinglist.</p>
 <p>If <em>dimensions</em> indicates a non-periodic system (i.e. all lengths
@@ -183,7 +190,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>dimensions</em></dt>
 <dd><p class="first last">list of box lengths and angles (in degrees) such as
 [A,B,C,alpha,beta,gamma]</p>
@@ -191,7 +198,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">numpy 3x3 array B, with B[0] = first box vector,
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">numpy 3x3 array B, with B[0] = first box vector,
 B[1] = second vector, B[2] third box vector.</p>
 </td>
 </tr>
@@ -202,21 +209,22 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 <p class="last">The first vector is always pointing along the X-axis
 i.e. parallel to (1,0,0).</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>Null-vectors are returned for non-periodic (or missing) unit cell.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>Null-vectors are returned for non-periodic (or missing) unit cell.</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.mdamath.box_volume">
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">box_volume</tt><big>(</big><em>dimensions</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#box_volume"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.box_volume" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">box_volume</code><span class="sig-paren">(</span><em>dimensions</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#box_volume"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.box_volume" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return the volume of the unitcell described by <em>dimensions</em>.</p>
 <p>The volume is computed as <cite>det(x1,x2,x2)</cite> where the xi are the
-triclinic box vectors from <a class="reference internal" href="#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><tt class="xref py py-func docutils literal"><span class="pre">triclinic_vectors()</span></tt></a>.</p>
+triclinic box vectors from <a class="reference internal" href="#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><code class="xref py py-func docutils literal"><span class="pre">triclinic_vectors()</span></code></a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>dimensions</em></dt>
 <dd><p class="first last">list of box lengths and angles (in degrees) such as
 [A,B,C,alpha,beta,gamma]</p>
@@ -224,7 +232,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">numpy 3x3 array B, with B[0] = first box vector,
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">numpy 3x3 array B, with B[0] = first box vector,
 B[1] = second vector, B[2] third box vector.</p>
 </td>
 </tr>
@@ -234,22 +242,22 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 
 <dl class="function">
 <dt id="MDAnalysis.lib.mdamath.make_whole">
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">make_whole</tt><big>(</big><em>atomgroup</em>, <em>reference_atom=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#make_whole"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.make_whole" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">make_whole</code><span class="sig-paren">(</span><em>atomgroup</em>, <em>reference_atom=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#make_whole"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.mdamath.make_whole" title="Permalink to this definition">¶</a></dt>
 <dd><p>Move all atoms in a single molecule so that bonds don&#8217;t split over images</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>atomgroup</em></dt>
-<dd><p class="first last">The <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> to work with.
+<dd><p class="first last">The <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> to work with.
 The positions of this are modified in place.  All these atoms
 must belong in the same molecule.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>reference_atom</em></dt>
 <dd><p class="first last">The atom around which all other atoms will be moved.
 Defaults to atom 0 in the atomgroup.</p>
@@ -257,13 +265,13 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first"><tt class="docutils literal"><span class="pre">None</span></tt>.  Atom positions are modified in place</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><code class="docutils literal"><span class="pre">None</span></code>.  Atom positions are modified in place</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
 <dt><cite>NoDataError</cite></dt>
 <dd><p class="first last">if there are no bonds present.
-(See <a class="reference internal" href="../topology/core.html#MDAnalysis.topology.core.guess_bonds" title="MDAnalysis.topology.core.guess_bonds"><tt class="xref py py-func docutils literal"><span class="pre">guess_bonds()</span></tt></a>)</p>
+(See <a class="reference internal" href="../topology/core.html#MDAnalysis.topology.core.guess_bonds" title="MDAnalysis.topology.core.guess_bonds"><code class="xref py py-func docutils literal"><span class="pre">guess_bonds()</span></code></a>)</p>
 </dd>
 <dt><cite>ValueError</cite></dt>
 <dd><p class="first last">if the algorithm fails to work.  This is usually
@@ -279,7 +287,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 unit cell, causing breaks mid molecule, with the molecule then appearing
 on either side of the unit cell. This is problematic for operations
 such as calculating the center of mass of the molecule.</p>
-<div class="highlight-python"><pre>+-----------+     +-----------+
+<div class="highlight-python"><div class="highlight"><pre>+-----------+     +-----------+
 |           |     |           |
 | 6       3 |     |         3 | 6
 | !       ! |     |         ! | !
@@ -287,7 +295,8 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 | !       ! |     |         ! | !
 | 7       4 |     |         4 | 7
 |           |     |           |
-+-----------+     +-----------+</pre>
++-----------+     +-----------+
+</pre></div>
 </div>
 <p>Usage:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">MDAnalysis.util.mdamath</span> <span class="kn">import</span> <span class="n">make_whole</span>
@@ -313,31 +322,34 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 <p class="first admonition-title">Note</p>
 <p class="last">Only orthogonal boxes are currently supported</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">angle</tt><big>(</big><em>a</em>, <em>b</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#angle"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">angle</code><span class="sig-paren">(</span><em>a</em>, <em>b</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#angle"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Returns the angle between two vectors in radians</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">box_volume</tt><big>(</big><em>dimensions</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#box_volume"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">box_volume</code><span class="sig-paren">(</span><em>dimensions</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#box_volume"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Return the volume of the unitcell described by <em>dimensions</em>.</p>
 <p>The volume is computed as <cite>det(x1,x2,x2)</cite> where the xi are the
-triclinic box vectors from <a class="reference internal" href="#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><tt class="xref py py-func docutils literal"><span class="pre">triclinic_vectors()</span></tt></a>.</p>
+triclinic box vectors from <a class="reference internal" href="#MDAnalysis.lib.mdamath.triclinic_vectors" title="MDAnalysis.lib.mdamath.triclinic_vectors"><code class="xref py py-func docutils literal"><span class="pre">triclinic_vectors()</span></code></a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>dimensions</em></dt>
 <dd><p class="first last">list of box lengths and angles (in degrees) such as
 [A,B,C,alpha,beta,gamma]</p>
@@ -345,7 +357,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">numpy 3x3 array B, with B[0] = first box vector,
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">numpy 3x3 array B, with B[0] = first box vector,
 B[1] = second vector, B[2] third box vector.</p>
 </td>
 </tr>
@@ -355,41 +367,44 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">dihedral</tt><big>(</big><em>ab</em>, <em>bc</em>, <em>cd</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#dihedral"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">dihedral</code><span class="sig-paren">(</span><em>ab</em>, <em>bc</em>, <em>cd</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#dihedral"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Returns the dihedral angle in radians between vectors connecting A,B,C,D.</p>
 <p>The dihedral measures the rotation around bc:</p>
-<div class="highlight-python"><pre>  ab
+<div class="highlight-python"><div class="highlight"><pre>  ab
 A----&gt;B
        \ bc
-       _\'
+       _\&#39;
          C----&gt;D
-           cd</pre>
+           cd
+</pre></div>
 </div>
 <p>The dihedral angle is restricted to the range -π &lt;= x &lt;= π.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">make_whole</tt><big>(</big><em>atomgroup</em>, <em>reference_atom=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#make_whole"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">make_whole</code><span class="sig-paren">(</span><em>atomgroup</em>, <em>reference_atom=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#make_whole"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Move all atoms in a single molecule so that bonds don&#8217;t split over images</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>atomgroup</em></dt>
-<dd><p class="first last">The <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> to work with.
+<dd><p class="first last">The <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> to work with.
 The positions of this are modified in place.  All these atoms
 must belong in the same molecule.</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>reference_atom</em></dt>
 <dd><p class="first last">The atom around which all other atoms will be moved.
 Defaults to atom 0 in the atomgroup.</p>
@@ -397,13 +412,13 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><p class="first"><tt class="docutils literal"><span class="pre">None</span></tt>.  Atom positions are modified in place</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><code class="docutils literal"><span class="pre">None</span></code>.  Atom positions are modified in place</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
 <dt><cite>NoDataError</cite></dt>
 <dd><p class="first last">if there are no bonds present.
-(See <a class="reference internal" href="../topology/core.html#MDAnalysis.topology.core.guess_bonds" title="MDAnalysis.topology.core.guess_bonds"><tt class="xref py py-func docutils literal"><span class="pre">guess_bonds()</span></tt></a>)</p>
+(See <a class="reference internal" href="../topology/core.html#MDAnalysis.topology.core.guess_bonds" title="MDAnalysis.topology.core.guess_bonds"><code class="xref py py-func docutils literal"><span class="pre">guess_bonds()</span></code></a>)</p>
 </dd>
 <dt><cite>ValueError</cite></dt>
 <dd><p class="first last">if the algorithm fails to work.  This is usually
@@ -419,7 +434,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 unit cell, causing breaks mid molecule, with the molecule then appearing
 on either side of the unit cell. This is problematic for operations
 such as calculating the center of mass of the molecule.</p>
-<div class="highlight-python"><pre>+-----------+     +-----------+
+<div class="highlight-python"><div class="highlight"><pre>+-----------+     +-----------+
 |           |     |           |
 | 6       3 |     |         3 | 6
 | !       ! |     |         ! | !
@@ -427,7 +442,8 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 | !       ! |     |         ! | !
 | 7       4 |     |         4 | 7
 |           |     |           |
-+-----------+     +-----------+</pre>
++-----------+     +-----------+
+</pre></div>
 </div>
 <p>Usage:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">MDAnalysis.util.mdamath</span> <span class="kn">import</span> <span class="n">make_whole</span>
@@ -453,47 +469,51 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 <p class="first admonition-title">Note</p>
 <p class="last">Only orthogonal boxes are currently supported</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">norm</tt><big>(</big><em>v</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#norm"><span class="viewcode-link">[source]</span></a></dt>
-<dd><p>Returns the length of a vector, <tt class="docutils literal"><span class="pre">sqrt(v.v)</span></tt>.</p>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">norm</code><span class="sig-paren">(</span><em>v</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#norm"><span class="viewcode-link">[source]</span></a></dt>
+<dd><p>Returns the length of a vector, <code class="docutils literal"><span class="pre">sqrt(v.v)</span></code>.</p>
 <div class="math">
 \[v = \sqrt{\mathbf{v}\cdot\mathbf{v}}\]</div>
-<p>Faster than <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.norm.html#numpy.linalg.norm" title="(in NumPy v1.9)"><tt class="xref py py-func docutils literal"><span class="pre">numpy.linalg.norm()</span></tt></a> because no frills.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+<p>Faster than <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.norm.html#numpy.linalg.norm" title="(in NumPy v1.9)"><code class="xref py py-func docutils literal"><span class="pre">numpy.linalg.norm()</span></code></a> because no frills.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">normal</tt><big>(</big><em>vec1</em>, <em>vec2</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#normal"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">normal</code><span class="sig-paren">(</span><em>vec1</em>, <em>vec2</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#normal"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Returns the unit vector normal to two vectors.</p>
 <div class="math">
 \[\hat{\mathbf{n}} = \frac{\mathbf{v}_1 \times \mathbf{v}_2}{|\mathbf{v}_1 \times \mathbf{v}_2|}\]</div>
 <p>If the two vectors are collinear, the vector <span class="math">\(\mathbf{0}\)</span> is returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">stp</tt><big>(</big><em>vec1</em>, <em>vec2</em>, <em>vec3</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#stp"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">stp</code><span class="sig-paren">(</span><em>vec1</em>, <em>vec2</em>, <em>vec3</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#stp"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Takes the scalar triple product of three vectors.</p>
 <p>Returns the volume <em>V</em> of the parallel epiped spanned by the three
 vectors</p>
 <div class="math">
 \[V = \mathbf{v}_3 \cdot (\mathbf{v}_1 \times \mathbf{v}_2)\]</div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Moved into lib.mdamath</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">triclinic_box</tt><big>(</big><em>x</em>, <em>y</em>, <em>z</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#triclinic_box"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">triclinic_box</code><span class="sig-paren">(</span><em>x</em>, <em>y</em>, <em>z</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#triclinic_box"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Convert the three triclinic box vectors to [A,B,C,alpha,beta,gamma].</p>
 <p>Angles are in degrees.</p>
 <ul class="simple">
@@ -501,7 +521,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 <li>beta   = angle(x,z)</li>
 <li>gamma  = angle(x,y)</li>
 </ul>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">Definition of angles: <a class="reference external" href="http://en.wikipedia.org/wiki/Lattice_constant">http://en.wikipedia.org/wiki/Lattice_constant</a></p>
 </div>
@@ -509,7 +529,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 
 <dl class="function">
 <dt>
-<tt class="descclassname">MDAnalysis.lib.mdamath.</tt><tt class="descname">triclinic_vectors</tt><big>(</big><em>dimensions</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#triclinic_vectors"><span class="viewcode-link">[source]</span></a></dt>
+<code class="descclassname">MDAnalysis.lib.mdamath.</code><code class="descname">triclinic_vectors</code><span class="sig-paren">(</span><em>dimensions</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/mdamath.html#triclinic_vectors"><span class="viewcode-link">[source]</span></a></dt>
 <dd><p>Convert <cite>[A,B,C,alpha,beta,gamma]</cite> to a triclinic box representation.</p>
 <p>Original <a class="reference external" href="http://www.mail-archive.com/gmx-users&#64;gromacs.org/msg28032.html">code by Tsjerk Wassenaar</a> posted on the Gromacs mailinglist.</p>
 <p>If <em>dimensions</em> indicates a non-periodic system (i.e. all lengths
@@ -518,7 +538,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>dimensions</em></dt>
 <dd><p class="first last">list of box lengths and angles (in degrees) such as
 [A,B,C,alpha,beta,gamma]</p>
@@ -526,7 +546,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">numpy 3x3 array B, with B[0] = first box vector,
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">numpy 3x3 array B, with B[0] = first box vector,
 B[1] = second vector, B[2] third box vector.</p>
 </td>
 </tr>
@@ -537,8 +557,9 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
 <p class="last">The first vector is always pointing along the X-axis
 i.e. parallel to (1,0,0).</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>Null-vectors are returned for non-periodic (or missing) unit cell.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>Null-vectors are returned for non-periodic (or missing) unit cell.</p>
+</div>
 </dd></dl>
 
 </div>
@@ -549,7 +570,7 @@ <h1>9.5. Mathematical helper functions &#8212; <a class="reference internal" hre
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -564,11 +585,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="log.html" title="9.4. Setting up logging — MDAnalysis.lib.log"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -578,7 +599,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/lib/parallel.html b/package/doc/html/documentation_pages/lib/parallel.html
index 9ef572e52b4..33994cae593 100644
--- a/package/doc/html/documentation_pages/lib/parallel.html
+++ b/package/doc/html/documentation_pages/lib/parallel.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>9.6. Parallel algorithms for MDAnalysis &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>9.6. Parallel algorithms for MDAnalysis &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
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       var DOCUMENTATION_OPTIONS = {
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-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="9. MDAnalysis library" href="../lib_modules.html" />
     <link rel="next" title="9.7. Homogeneous Transformation Matrices and Quaternions — MDAnalysis.lib.transformations" href="transformations.html" />
     <link rel="prev" title="9.5. Mathematical helper functions — MDAnalysis.lib.mdamath" href="mdamath.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="mdamath.html" title="9.5. Mathematical helper functions — MDAnalysis.lib.mdamath"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
       </ul>
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-      <div class="sphinxsidebar">
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         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -63,23 +61,25 @@ <h3>Navigation</h3>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
 <li><a class="reference internal" href="#">9.6. Parallel algorithms for MDAnalysis</a><ul>
-<li><a class="reference internal" href="#fast-parallel-distance-array-computation-mdanalysis-lib-parallel-distances">9.6.1. Fast parallel distance array computation &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.parallel.distances</span></tt></a></li>
+<li><a class="reference internal" href="#fast-parallel-distance-array-computation-mdanalysis-lib-parallel-distances">9.6.1. Fast parallel distance array computation &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.parallel.distances</span></code></a></li>
 </ul>
 </li>
 </ul>
 
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-                        title="previous chapter">9.5. Mathematical helper functions &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.lib.mdamath</span></tt></a></p>
+                        title="previous chapter">9.5. Mathematical helper functions &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.mdamath</span></code></a></p>
   <h4>Next topic</h4>
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-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/lib/parallel.txt"
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-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">9.7. Homogeneous Transformation Matrices and Quaternions &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.transformations</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/lib/parallel.txt"
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+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
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-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.lib.parallel"></span><div class="section" id="parallel-algorithms-for-mdanalysis">
 <h1>9.6. Parallel algorithms for MDAnalysis<a class="headerlink" href="#parallel-algorithms-for-mdanalysis" title="Permalink to this headline">¶</a></h1>
-<p>The <a class="reference internal" href="#module-MDAnalysis.lib.parallel" title="MDAnalysis.lib.parallel"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.parallel</span></tt></a> module contains implementations of
+<p>The <a class="reference internal" href="#module-MDAnalysis.lib.parallel" title="MDAnalysis.lib.parallel"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.parallel</span></code></a> module contains implementations of
 standard functions that can make use of parallelization available on
 modern multi-core processors.</p>
 <div class="admonition warning">
@@ -112,7 +112,7 @@ <h1>9.6. Parallel algorithms for MDAnalysis<a class="headerlink" href="#parallel
 incompatibilities or less features than the serial code.</p>
 </div>
 <span class="target" id="module-MDAnalysis.lib.parallel.distances"></span><div class="section" id="fast-parallel-distance-array-computation-mdanalysis-lib-parallel-distances">
-<h2>9.6.1. Fast parallel distance array computation &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.parallel.distances" title="MDAnalysis.lib.parallel.distances"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.parallel.distances</span></tt></a><a class="headerlink" href="#fast-parallel-distance-array-computation-mdanalysis-lib-parallel-distances" title="Permalink to this headline">¶</a></h2>
+<h2>9.6.1. Fast parallel distance array computation &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.parallel.distances" title="MDAnalysis.lib.parallel.distances"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.parallel.distances</span></code></a><a class="headerlink" href="#fast-parallel-distance-array-computation-mdanalysis-lib-parallel-distances" title="Permalink to this headline">¶</a></h2>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -125,8 +125,8 @@ <h2>9.6.1. Fast parallel distance array computation &#8212; <a class="reference
 </tr>
 </tbody>
 </table>
-<p>A fast, parallel <a class="reference internal" href="#MDAnalysis.lib.parallel.distances.distance_array" title="MDAnalysis.lib.parallel.distances.distance_array"><tt class="xref py py-func docutils literal"><span class="pre">distance_array()</span></tt></a> function as a substitute for
-<a class="reference internal" href="distances.html#MDAnalysis.lib.distances.distance_array" title="MDAnalysis.lib.distances.distance_array"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.distances.distance_array()</span></tt></a>; implemented with
+<p>A fast, parallel <a class="reference internal" href="#MDAnalysis.lib.parallel.distances.distance_array" title="MDAnalysis.lib.parallel.distances.distance_array"><code class="xref py py-func docutils literal"><span class="pre">distance_array()</span></code></a> function as a substitute for
+<a class="reference internal" href="distances.html#MDAnalysis.lib.distances.distance_array" title="MDAnalysis.lib.distances.distance_array"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.distances.distance_array()</span></code></a>; implemented with
 <a class="reference external" href="http://docs.cython.org/src/userguide/parallelism.html">Cython Parallelism</a>. For development notes see the comments for
 <a class="reference external" href="http://issues.mdanalysis.org/80">Issue 80</a>.</p>
 <p>Load the module with</p>
@@ -135,13 +135,13 @@ <h2>9.6.1. Fast parallel distance array computation &#8212; <a class="reference
 </div>
 <dl class="function">
 <dt id="MDAnalysis.lib.parallel.distances.distance_array">
-<tt class="descclassname">MDAnalysis.lib.parallel.distances.</tt><tt class="descname">distance_array</tt><big>(</big><em>ref</em>, <em>conf</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><big>)</big><a class="headerlink" href="#MDAnalysis.lib.parallel.distances.distance_array" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculate all distances d_ij between the coordinates <tt class="docutils literal"><span class="pre">ref[i]</span></tt> and
-<tt class="docutils literal"><span class="pre">conf[j]</span></tt> in the numpy arrays <em>ref</em> and <em>conf</em>.</p>
+<code class="descclassname">MDAnalysis.lib.parallel.distances.</code><code class="descname">distance_array</code><span class="sig-paren">(</span><em>ref</em>, <em>conf</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.lib.parallel.distances.distance_array" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculate all distances d_ij between the coordinates <code class="docutils literal"><span class="pre">ref[i]</span></code> and
+<code class="docutils literal"><span class="pre">conf[j]</span></code> in the numpy arrays <em>ref</em> and <em>conf</em>.</p>
 <p>This is a parallelized version that will automatically decide on
 how many threads to run.</p>
 <p>Periodic boundary conditions can be taken into account if the box
-vectors are provided in the 3x3 matrix <em>box</em>. The default <tt class="docutils literal"><span class="pre">None</span></tt>
+vectors are provided in the 3x3 matrix <em>box</em>. The default <code class="docutils literal"><span class="pre">None</span></code>
 calculates simple distances.</p>
 <p>A pre-allocated array can be supplied as <em>results</em>.</p>
 <div class="admonition warning">
@@ -149,29 +149,31 @@ <h2>9.6.1. Fast parallel distance array computation &#8212; <a class="reference
 <p class="last">Only orthorhombic boxes are supported for <em>box</em>, anything else will
 produce wrong results.</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.parallel.distances.distance_array_serial">
-<tt class="descclassname">MDAnalysis.lib.parallel.distances.</tt><tt class="descname">distance_array_serial</tt><big>(</big><em>ref</em>, <em>conf</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><big>)</big><a class="headerlink" href="#MDAnalysis.lib.parallel.distances.distance_array_serial" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.parallel.distances.</code><code class="descname">distance_array_serial</code><span class="sig-paren">(</span><em>ref</em>, <em>conf</em><span class="optional">[</span>, <em>box</em><span class="optional">[</span>, <em>result</em><span class="optional">]</span><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.lib.parallel.distances.distance_array_serial" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate all distances d_ij between the coordinates ref[i] and
 conf[j] in the numpy arrays <em>ref</em> and <em>conf</em>.</p>
 <p>Periodic boundary conditions can be taken into account if the box
-vectors are provided in the 3x3 matrix <em>box</em>. The default <tt class="docutils literal"><span class="pre">None</span></tt>
+vectors are provided in the 3x3 matrix <em>box</em>. The default <code class="docutils literal"><span class="pre">None</span></code>
 calculates simple distances.</p>
 <p>A pre-allocated array can be supplied as <em>results</em>.</p>
 <p>Serial version (to check the parallel version). This version is
 slightly slower than the regular serial (pure C)
-<a class="reference internal" href="distances.html#MDAnalysis.lib.distances.distance_array" title="MDAnalysis.lib.distances.distance_array"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.distances.distance_array()</span></tt></a> function.</p>
+<a class="reference internal" href="distances.html#MDAnalysis.lib.distances.distance_array" title="MDAnalysis.lib.distances.distance_array"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.lib.distances.distance_array()</span></code></a> function.</p>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
 <p class="last">Only orthorhombic boxes are supported for <em>box</em>, anything else will
 produce wrong results.</p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 </div>
@@ -183,7 +185,7 @@ <h2>9.6.1. Fast parallel distance array computation &#8212; <a class="reference
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -198,11 +200,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="mdamath.html" title="9.5. Mathematical helper functions — MDAnalysis.lib.mdamath"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -212,7 +214,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/lib/qcprot.html b/package/doc/html/documentation_pages/lib/qcprot.html
index 94b09b4e6d6..db8f8bba730 100644
--- a/package/doc/html/documentation_pages/lib/qcprot.html
+++ b/package/doc/html/documentation_pages/lib/qcprot.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>9.8. Fast QCP RMSD structure alignment — MDAnalysis.lib.qcprot &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>9.8. Fast QCP RMSD structure alignment — MDAnalysis.lib.qcprot &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
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-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="9. MDAnalysis library" href="../lib_modules.html" />
     <link rel="next" title="9.9. Helper functions — MDAnalysis.lib.util" href="util.html" />
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              accesskey="P">previous</a> |</li>
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+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
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   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">9.8. Fast QCP RMSD structure alignment &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></tt></a><ul>
+<li><a class="reference internal" href="#">9.8. Fast QCP RMSD structure alignment &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></code></a><ul>
 <li><a class="reference internal" href="#references">9.8.1. References</a></li>
 <li><a class="reference internal" href="#functions">9.8.2. Functions</a></li>
 </ul>
@@ -71,16 +69,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
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-                        title="previous chapter">9.7. Homogeneous Transformation Matrices and Quaternions &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.lib.transformations</span></tt></a></p>
+                        title="previous chapter">9.7. Homogeneous Transformation Matrices and Quaternions &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.transformations</span></code></a></p>
   <h4>Next topic</h4>
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-  </ul>
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+                        title="next chapter">9.9. Helper functions &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.util</span></code></a></p>
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+    <h3>This Page</h3>
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   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -99,10 +99,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
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-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.lib.qcprot"></span><div class="section" id="fast-qcp-rmsd-structure-alignment-mdanalysis-lib-qcprot">
-<h1>9.8. Fast QCP RMSD structure alignment &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.qcprot" title="MDAnalysis.lib.qcprot"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></tt></a><a class="headerlink" href="#fast-qcp-rmsd-structure-alignment-mdanalysis-lib-qcprot" title="Permalink to this headline">¶</a></h1>
+<h1>9.8. Fast QCP RMSD structure alignment &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.qcprot" title="MDAnalysis.lib.qcprot"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></code></a><a class="headerlink" href="#fast-qcp-rmsd-structure-alignment-mdanalysis-lib-qcprot" title="Permalink to this headline">¶</a></h1>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -119,15 +119,15 @@ <h1>9.8. Fast QCP RMSD structure alignment &#8212; <a class="reference internal"
 </table>
 <p><a class="reference external" href="https://github.com/synapticarbors/pyqcprot">PyQCPROT</a> is a python/cython implementation of Douglas Theobald&#8217;s QCP
 method for calculating the minimum RMSD between two structures
-<a class="reference internal" href="#theobald2005">[Theobald2005]</a> and determining the optimal least-squares rotation
-matrix <a class="reference internal" href="#liu2010">[Liu2010]</a>.</p>
+<a class="reference internal" href="#theobald2005" id="id1">[Theobald2005]</a> and determining the optimal least-squares rotation
+matrix <a class="reference internal" href="#liu2010" id="id2">[Liu2010]</a>.</p>
 <p>A full description of the method, along with the original C implementation can
 be found at <a class="reference external" href="http://theobald.brandeis.edu/qcp/">http://theobald.brandeis.edu/qcp/</a></p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last">The <a class="reference internal" href="#MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix" title="MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix"><tt class="xref py py-func docutils literal"><span class="pre">CalcRMSDRotationalMatrix()</span></tt></a> function is used in
-<a class="reference internal" href="../analysis/align.html#module-MDAnalysis.analysis.align" title="MDAnalysis.analysis.align"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.align</span></tt></a> and
-<tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.rmsd</span></tt>.</p>
+<p class="last">The <a class="reference internal" href="#MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix" title="MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix"><code class="xref py py-func docutils literal"><span class="pre">CalcRMSDRotationalMatrix()</span></code></a> function is used in
+<a class="reference internal" href="../analysis/align.html#module-MDAnalysis.analysis.align" title="MDAnalysis.analysis.align"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.align</span></code></a> and
+<code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.rmsd</span></code>.</p>
 </div>
 <div class="section" id="references">
 <h2>9.8.1. References<a class="headerlink" href="#references" title="Permalink to this headline">¶</a></h2>
@@ -152,10 +152,10 @@ <h2>9.8.1. References<a class="headerlink" href="#references" title="Permalink t
 </div>
 <div class="section" id="functions">
 <h2>9.8.2. Functions<a class="headerlink" href="#functions" title="Permalink to this headline">¶</a></h2>
-<p>Users will typically use the <a class="reference internal" href="#MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix" title="MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix"><tt class="xref py py-func docutils literal"><span class="pre">CalcRMSDRotationalMatrix()</span></tt></a> function.</p>
+<p>Users will typically use the <a class="reference internal" href="#MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix" title="MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix"><code class="xref py py-func docutils literal"><span class="pre">CalcRMSDRotationalMatrix()</span></code></a> function.</p>
 <dl class="function">
 <dt id="MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix">
-<tt class="descclassname">MDAnalysis.lib.qcprot.</tt><tt class="descname">CalcRMSDRotationalMatrix</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.qcprot.</code><code class="descname">CalcRMSDRotationalMatrix</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate the RMSD &amp; rotational matrix.</p>
 <dl class="docutils">
 <dt>CalcRMSDRotationalMatrix(ref, conf, N, rot, weights):</dt>
@@ -194,10 +194,10 @@ <h2>9.8.2. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.qcprot.InnerProduct">
-<tt class="descclassname">MDAnalysis.lib.qcprot.</tt><tt class="descname">InnerProduct</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.lib.qcprot.InnerProduct" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.qcprot.</code><code class="descname">InnerProduct</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.lib.qcprot.InnerProduct" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate the inner product of two structures.</p>
 <p>InnerProduct(A, coords1, coords2, N, weight) &#8211;&gt; (G1+G2)/2</p>
-<p>If weight array is not <tt class="docutils literal"><span class="pre">None</span></tt>, calculate the weighted inner product.</p>
+<p>If weight array is not <code class="docutils literal"><span class="pre">None</span></code>, calculate the weighted inner product.</p>
 <blockquote>
 <div><table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -218,7 +218,7 @@ <h2>9.8.2. Functions<a class="headerlink" href="#functions" title="Permalink to
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><ul class="first last simple">
-<li>(G1 + G2) * 0.5; used as E0 in function <a class="reference internal" href="#MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation" title="MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation"><tt class="xref py py-func docutils literal"><span class="pre">FastCalcRMSDAndRotation()</span></tt></a></li>
+<li>(G1 + G2) * 0.5; used as E0 in function <a class="reference internal" href="#MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation" title="MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation"><code class="xref py py-func docutils literal"><span class="pre">FastCalcRMSDAndRotation()</span></code></a></li>
 </ul>
 </td>
 </tr>
@@ -232,8 +232,9 @@ <h2>9.8.2. Functions<a class="headerlink" href="#functions" title="Permalink to
 <li><p class="first">Please note how the structure coordinates are stored as 3xN arrays,
 not Nx3 arrays as is also commonly used. The difference is
 something like this for storage of a structure with 8 atoms:</p>
-<div class="highlight-python"><pre>Nx3: xyzxyzxyzxyzxyzxyzxyzxyz
-3xN: xxxxxxxxyyyyyyyyzzzzzzzz</pre>
+<div class="highlight-python"><div class="highlight"><pre>Nx3: xyzxyzxyzxyzxyzxyzxyzxyz
+3xN: xxxxxxxxyyyyyyyyzzzzzzzz
+</pre></div>
 </div>
 </li>
 </ol>
@@ -243,7 +244,7 @@ <h2>9.8.2. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation">
-<tt class="descclassname">MDAnalysis.lib.qcprot.</tt><tt class="descname">FastCalcRMSDAndRotation</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.qcprot.</code><code class="descname">FastCalcRMSDAndRotation</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate the RMSD, and/or the optimal rotation matrix.</p>
 <p>FastCalcRMSDAndRotation(rot, A, E0, N)</p>
 <blockquote>
@@ -285,7 +286,7 @@ <h2>9.8.2. Functions<a class="headerlink" href="#functions" title="Permalink to
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
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              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
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@@ -314,7 +315,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/lib/transformations.html b/package/doc/html/documentation_pages/lib/transformations.html
index dc01d9134a9..452f99c270d 100644
--- a/package/doc/html/documentation_pages/lib/transformations.html
+++ b/package/doc/html/documentation_pages/lib/transformations.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
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     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>9.7. Homogeneous Transformation Matrices and Quaternions — MDAnalysis.lib.transformations &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>9.7. Homogeneous Transformation Matrices and Quaternions — MDAnalysis.lib.transformations &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
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@@ -27,16 +25,16 @@
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     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
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     <link rel="next" title="9.8. Fast QCP RMSD structure alignment — MDAnalysis.lib.qcprot" href="qcprot.html" />
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              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
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         <div class="sphinxsidebarwrapper">
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               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">9.7. Homogeneous Transformation Matrices and Quaternions &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.transformations</span></tt></a><ul>
+<li><a class="reference internal" href="#">9.7. Homogeneous Transformation Matrices and Quaternions &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.transformations</span></code></a><ul>
 <li><a class="reference internal" href="#requirements">9.7.1. Requirements</a></li>
 <li><a class="reference internal" href="#notes">9.7.2. Notes</a></li>
 <li><a class="reference internal" href="#references">9.7.3. References</a></li>
@@ -77,13 +75,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">9.6. Parallel algorithms for MDAnalysis</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="qcprot.html"
-                        title="next chapter">9.8. Fast QCP RMSD structure alignment &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/lib/transformations.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">9.8. Fast QCP RMSD structure alignment &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/lib/transformations.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -102,10 +102,10 @@ <h3>Quick search</h3>
     <div class="document">
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+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.lib.transformations"></span><div class="section" id="homogeneous-transformation-matrices-and-quaternions-mdanalysis-lib-transformations">
-<h1>9.7. Homogeneous Transformation Matrices and Quaternions &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.transformations" title="MDAnalysis.lib.transformations"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.transformations</span></tt></a><a class="headerlink" href="#homogeneous-transformation-matrices-and-quaternions-mdanalysis-lib-transformations" title="Permalink to this headline">¶</a></h1>
+<h1>9.7. Homogeneous Transformation Matrices and Quaternions &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.transformations" title="MDAnalysis.lib.transformations"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.transformations</span></code></a><a class="headerlink" href="#homogeneous-transformation-matrices-and-quaternions-mdanalysis-lib-transformations" title="Permalink to this headline">¶</a></h1>
 <p>A library for calculating 4x4 matrices for translating, rotating, reflecting,
 scaling, shearing, projecting, orthogonalizing, and superimposing arrays of
 3D homogeneous coordinates as well as for converting between rotation matrices,
@@ -249,12 +249,13 @@ <h2>9.7.4. Examples<a class="headerlink" href="#examples" title="Permalink to th
 </div>
 <div class="section" id="functions">
 <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to this headline">¶</a></h2>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Transformations library moved from MDAnalysis.core.transformations to
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Transformations library moved from MDAnalysis.core.transformations to
 MDAnalysis.lib.transformations</p>
+</div>
 <dl class="class">
 <dt id="MDAnalysis.lib.transformations.Arcball">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">Arcball</tt><big>(</big><em>initial=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">Arcball</code><span class="sig-paren">(</span><em>initial=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball" title="Permalink to this definition">¶</a></dt>
 <dd><p>Virtual Trackball Control.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">ball</span> <span class="o">=</span> <span class="n">Arcball</span><span class="p">()</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">ball</span> <span class="o">=</span> <span class="n">Arcball</span><span class="p">(</span><span class="n">initial</span><span class="o">=</span><span class="n">numpy</span><span class="o">.</span><span class="n">identity</span><span class="p">(</span><span class="mi">4</span><span class="p">))</span>
@@ -280,37 +281,37 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 <p>initial : quaternion or rotation matrix</p>
 <dl class="method">
 <dt id="MDAnalysis.lib.transformations.Arcball.down">
-<tt class="descname">down</tt><big>(</big><em>point</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.down"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.down" title="Permalink to this definition">¶</a></dt>
+<code class="descname">down</code><span class="sig-paren">(</span><em>point</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.down"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.down" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set initial cursor window coordinates and pick constrain-axis.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.transformations.Arcball.drag">
-<tt class="descname">drag</tt><big>(</big><em>point</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.drag"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.drag" title="Permalink to this definition">¶</a></dt>
+<code class="descname">drag</code><span class="sig-paren">(</span><em>point</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.drag"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.drag" title="Permalink to this definition">¶</a></dt>
 <dd><p>Update current cursor window coordinates.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.transformations.Arcball.getconstrain">
-<tt class="descname">getconstrain</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.getconstrain"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.getconstrain" title="Permalink to this definition">¶</a></dt>
+<code class="descname">getconstrain</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.getconstrain"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.getconstrain" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return state of constrain to axis mode.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.transformations.Arcball.matrix">
-<tt class="descname">matrix</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.matrix" title="Permalink to this definition">¶</a></dt>
+<code class="descname">matrix</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.matrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return homogeneous rotation matrix.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.transformations.Arcball.next">
-<tt class="descname">next</tt><big>(</big><em>acceleration=0.0</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.next"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.next" title="Permalink to this definition">¶</a></dt>
+<code class="descname">next</code><span class="sig-paren">(</span><em>acceleration=0.0</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.next"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.next" title="Permalink to this definition">¶</a></dt>
 <dd><p>Continue rotation in direction of last drag.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.transformations.Arcball.place">
-<tt class="descname">place</tt><big>(</big><em>center</em>, <em>radius</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.place"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.place" title="Permalink to this definition">¶</a></dt>
+<code class="descname">place</code><span class="sig-paren">(</span><em>center</em>, <em>radius</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.place"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.place" title="Permalink to this definition">¶</a></dt>
 <dd><p>Place Arcball, e.g. when window size changes.</p>
 <dl class="docutils">
 <dt>center <span class="classifier-delimiter">:</span> <span class="classifier">sequence[2]</span></dt>
@@ -322,13 +323,13 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="method">
 <dt id="MDAnalysis.lib.transformations.Arcball.setaxes">
-<tt class="descname">setaxes</tt><big>(</big><em>*axes</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.setaxes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.setaxes" title="Permalink to this definition">¶</a></dt>
+<code class="descname">setaxes</code><span class="sig-paren">(</span><em>*axes</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.setaxes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.setaxes" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set axes to constrain rotations.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.transformations.Arcball.setconstrain">
-<tt class="descname">setconstrain</tt><big>(</big><em>constrain</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.setconstrain"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.setconstrain" title="Permalink to this definition">¶</a></dt>
+<code class="descname">setconstrain</code><span class="sig-paren">(</span><em>constrain</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#Arcball.setconstrain"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.Arcball.setconstrain" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set state of constrain to axis mode.</p>
 </dd></dl>
 
@@ -336,13 +337,13 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.arcball_nearest_axis">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">arcball_nearest_axis</tt><big>(</big><em>point</em>, <em>axes</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#arcball_nearest_axis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.arcball_nearest_axis" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">arcball_nearest_axis</code><span class="sig-paren">(</span><em>point</em>, <em>axes</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#arcball_nearest_axis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.arcball_nearest_axis" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return axis, which arc is nearest to point.</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.compose_matrix">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">compose_matrix</tt><big>(</big><em>scale=None</em>, <em>shear=None</em>, <em>angles=None</em>, <em>translate=None</em>, <em>perspective=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#compose_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.compose_matrix" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">compose_matrix</code><span class="sig-paren">(</span><em>scale=None</em>, <em>shear=None</em>, <em>angles=None</em>, <em>translate=None</em>, <em>perspective=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#compose_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.compose_matrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return transformation matrix from sequence of transformations.</p>
 <p>This is the inverse of the decompose_matrix function.</p>
 <dl class="docutils">
@@ -369,7 +370,7 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.concatenate_matrices">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">concatenate_matrices</tt><big>(</big><em>*matrices</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#concatenate_matrices"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.concatenate_matrices" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">concatenate_matrices</code><span class="sig-paren">(</span><em>*matrices</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#concatenate_matrices"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.concatenate_matrices" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return concatenation of series of transformation matrices.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">M</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">rand</span><span class="p">(</span><span class="mi">16</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">((</span><span class="mi">4</span><span class="p">,</span> <span class="mi">4</span><span class="p">))</span> <span class="o">-</span> <span class="mf">0.5</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">numpy</span><span class="o">.</span><span class="n">allclose</span><span class="p">(</span><span class="n">M</span><span class="p">,</span> <span class="n">concatenate_matrices</span><span class="p">(</span><span class="n">M</span><span class="p">))</span>
@@ -382,7 +383,7 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.decompose_matrix">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">decompose_matrix</tt><big>(</big><em>matrix</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#decompose_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.decompose_matrix" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">decompose_matrix</code><span class="sig-paren">(</span><em>matrix</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#decompose_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.decompose_matrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return sequence of transformations from transformation matrix.</p>
 <dl class="docutils">
 <dt>matrix <span class="classifier-delimiter">:</span> <span class="classifier">array_like</span></dt>
@@ -415,7 +416,7 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.euler_from_quaternion">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">euler_from_quaternion</tt><big>(</big><em>quaternion</em>, <em>axes='sxyz'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#euler_from_quaternion"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.euler_from_quaternion" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">euler_from_quaternion</code><span class="sig-paren">(</span><em>quaternion</em>, <em>axes='sxyz'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#euler_from_quaternion"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.euler_from_quaternion" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return Euler angles from quaternion for specified axis sequence.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">angles</span> <span class="o">=</span> <span class="n">euler_from_quaternion</span><span class="p">([</span><span class="mf">0.99810947</span><span class="p">,</span> <span class="mf">0.06146124</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">])</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">numpy</span><span class="o">.</span><span class="n">allclose</span><span class="p">(</span><span class="n">angles</span><span class="p">,</span> <span class="p">[</span><span class="mf">0.123</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">])</span>
@@ -426,7 +427,7 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.projection_from_matrix">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">projection_from_matrix</tt><big>(</big><em>matrix</em>, <em>pseudo=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#projection_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.projection_from_matrix" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">projection_from_matrix</code><span class="sig-paren">(</span><em>matrix</em>, <em>pseudo=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#projection_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.projection_from_matrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return projection plane and perspective point from projection matrix.</p>
 <p>Return values are same as arguments for projection_matrix function:
 point, normal, direction, perspective, and pseudo.</p>
@@ -460,7 +461,7 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.quaternion_imag">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">quaternion_imag</tt><big>(</big><em>quaternion</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#quaternion_imag"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.quaternion_imag" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">quaternion_imag</code><span class="sig-paren">(</span><em>quaternion</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#quaternion_imag"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.quaternion_imag" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return imaginary part of quaternion.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">quaternion_imag</span><span class="p">([</span><span class="mf">3.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">2.0</span><span class="p">])</span>
 <span class="go">[0.0, 1.0, 2.0]</span>
@@ -470,7 +471,7 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.quaternion_real">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">quaternion_real</tt><big>(</big><em>quaternion</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#quaternion_real"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.quaternion_real" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">quaternion_real</code><span class="sig-paren">(</span><em>quaternion</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#quaternion_real"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.quaternion_real" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return real part of quaternion.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">quaternion_real</span><span class="p">([</span><span class="mf">3.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">2.0</span><span class="p">])</span>
 <span class="go">3.0</span>
@@ -480,7 +481,7 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.reflection_from_matrix">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">reflection_from_matrix</tt><big>(</big><em>matrix</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#reflection_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.reflection_from_matrix" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">reflection_from_matrix</code><span class="sig-paren">(</span><em>matrix</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#reflection_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.reflection_from_matrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return mirror plane point and normal vector from reflection matrix.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">v0</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">-</span> <span class="mf">0.5</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">v1</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">-</span> <span class="mf">0.5</span>
@@ -495,7 +496,7 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.rotation_from_matrix">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">rotation_from_matrix</tt><big>(</big><em>matrix</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#rotation_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.rotation_from_matrix" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">rotation_from_matrix</code><span class="sig-paren">(</span><em>matrix</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#rotation_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.rotation_from_matrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return rotation angle and axis from rotation matrix.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">angle</span> <span class="o">=</span> <span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">()</span> <span class="o">-</span> <span class="mf">0.5</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">math</span><span class="o">.</span><span class="n">pi</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">direc</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">-</span> <span class="mf">0.5</span>
@@ -511,13 +512,13 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.rotaxis">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">rotaxis</tt><big>(</big><em>a</em>, <em>b</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#rotaxis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.rotaxis" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">rotaxis</code><span class="sig-paren">(</span><em>a</em>, <em>b</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#rotaxis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.rotaxis" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return the rotation axis to rotate vector a into b.</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.scale_from_matrix">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">scale_from_matrix</tt><big>(</big><em>matrix</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#scale_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.scale_from_matrix" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">scale_from_matrix</code><span class="sig-paren">(</span><em>matrix</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#scale_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.scale_from_matrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return scaling factor, origin and direction from scaling matrix.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">factor</span> <span class="o">=</span> <span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">()</span> <span class="o">*</span> <span class="mi">10</span> <span class="o">-</span> <span class="mi">5</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">origin</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">-</span> <span class="mf">0.5</span>
@@ -538,7 +539,7 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.shear_from_matrix">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">shear_from_matrix</tt><big>(</big><em>matrix</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#shear_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.shear_from_matrix" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">shear_from_matrix</code><span class="sig-paren">(</span><em>matrix</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#shear_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.shear_from_matrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return shear angle, direction and plane from shear matrix.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">angle</span> <span class="o">=</span> <span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">()</span> <span class="o">-</span> <span class="mf">0.5</span><span class="p">)</span> <span class="o">*</span> <span class="mi">4</span><span class="o">*</span><span class="n">math</span><span class="o">.</span><span class="n">pi</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">direct</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">-</span> <span class="mf">0.5</span>
@@ -555,7 +556,7 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
 
 <dl class="function">
 <dt id="MDAnalysis.lib.transformations.translation_from_matrix">
-<tt class="descclassname">MDAnalysis.lib.transformations.</tt><tt class="descname">translation_from_matrix</tt><big>(</big><em>matrix</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#translation_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.translation_from_matrix" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.transformations.</code><code class="descname">translation_from_matrix</code><span class="sig-paren">(</span><em>matrix</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/transformations.html#translation_from_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.transformations.translation_from_matrix" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return translation vector from translation matrix.</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">v0</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">-</span> <span class="mf">0.5</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">v1</span> <span class="o">=</span> <span class="n">translation_from_matrix</span><span class="p">(</span><span class="n">translation_matrix</span><span class="p">(</span><span class="n">v0</span><span class="p">))</span>
@@ -574,7 +575,7 @@ <h2>9.7.5. Functions<a class="headerlink" href="#functions" title="Permalink to
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -589,11 +590,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="parallel.html" title="9.6. Parallel algorithms for MDAnalysis"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -603,7 +604,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/lib/util.html b/package/doc/html/documentation_pages/lib/util.html
index b4d4e86378b..4bbbe89cbed 100644
--- a/package/doc/html/documentation_pages/lib/util.html
+++ b/package/doc/html/documentation_pages/lib/util.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>9.9. Helper functions — MDAnalysis.lib.util &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>9.9. Helper functions — MDAnalysis.lib.util &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="9. MDAnalysis library" href="../lib_modules.html" />
-    <link rel="next" title="10. Version information for MDAnalysis" href="../version.html" />
+    <link rel="next" title="10. Version information for MDAnalysis — MDAnalysis.version" href="../version.html" />
     <link rel="prev" title="9.8. Fast QCP RMSD structure alignment — MDAnalysis.lib.qcprot" href="qcprot.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -46,23 +44,23 @@ <h3>Navigation</h3>
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="../version.html" title="10. Version information for MDAnalysis"
+          <a href="../version.html" title="10. Version information for MDAnalysis — MDAnalysis.version"
              accesskey="N">next</a> |</li>
         <li class="right" >
           <a href="qcprot.html" title="9.8. Fast QCP RMSD structure alignment — MDAnalysis.lib.qcprot"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" accesskey="U">9. MDAnalysis library</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">9.9. Helper functions &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.util</span></tt></a><ul>
+<li><a class="reference internal" href="#">9.9. Helper functions &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.util</span></code></a><ul>
 <li><a class="reference internal" href="#files-and-directories">9.9.1. Files and directories</a></li>
 <li><a class="reference internal" href="#streams">9.9.2. Streams</a></li>
 <li><a class="reference internal" href="#containers-and-lists">9.9.3. Containers and lists</a></li>
@@ -76,16 +74,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="qcprot.html"
-                        title="previous chapter">9.8. Fast QCP RMSD structure alignment &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></tt></a></p>
+                        title="previous chapter">9.8. Fast QCP RMSD structure alignment &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="../version.html"
-                        title="next chapter">10. Version information for MDAnalysis</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/lib/util.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">10. Version information for MDAnalysis — <code class="docutils literal"><span class="pre">MDAnalysis.version</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/lib/util.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -104,34 +104,34 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.lib.util"></span><div class="section" id="helper-functions-mdanalysis-lib-util">
-<h1>9.9. Helper functions &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.util" title="MDAnalysis.lib.util"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.util</span></tt></a><a class="headerlink" href="#helper-functions-mdanalysis-lib-util" title="Permalink to this headline">¶</a></h1>
+<h1>9.9. Helper functions &#8212; <a class="reference internal" href="#module-MDAnalysis.lib.util" title="MDAnalysis.lib.util"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.util</span></code></a><a class="headerlink" href="#helper-functions-mdanalysis-lib-util" title="Permalink to this headline">¶</a></h1>
 <p>Small helper functions that don&#8217;t fit anywhere else.</p>
 <div class="section" id="files-and-directories">
 <h2>9.9.1. Files and directories<a class="headerlink" href="#files-and-directories" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.lib.util.filename">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">filename</tt><big>(</big><em>name</em>, <em>ext=None</em>, <em>keep=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#filename"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.filename" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">filename</code><span class="sig-paren">(</span><em>name</em>, <em>ext=None</em>, <em>keep=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#filename"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.filename" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return a new name that has suffix attached; replaces other extensions.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>name</em></dt>
 <dd><p class="first last">filename; extension is replaced unless keep=True;
-<em>name</em> can also be a <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><tt class="xref py py-class docutils literal"><span class="pre">NamedStream</span></tt></a> (and its
-<tt class="xref py py-attr docutils literal"><span class="pre">NamedStream.name</span></tt> will be changed accordingly)</p>
+<em>name</em> can also be a <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><code class="xref py py-class docutils literal"><span class="pre">NamedStream</span></code></a> (and its
+<code class="xref py py-attr docutils literal"><span class="pre">NamedStream.name</span></code> will be changed accordingly)</p>
 </dd>
 <dt><em>ext</em></dt>
 <dd><p class="first last">extension</p>
 </dd>
 <dt><em>keep</em></dt>
 <dd><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">False</span></tt>: replace existing extension with <em>ext</em>;</li>
-<li><tt class="docutils literal"><span class="pre">True</span></tt>: keep old extension if one existed</li>
+<li><code class="docutils literal"><span class="pre">False</span></code>: replace existing extension with <em>ext</em>;</li>
+<li><code class="docutils literal"><span class="pre">True</span></code>: keep old extension if one existed</li>
 </ul>
 </dd>
 </dl>
@@ -139,78 +139,101 @@ <h2>9.9.1. Files and directories<a class="headerlink" href="#files-and-directori
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Also permits <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><tt class="xref py py-class docutils literal"><span class="pre">NamedStream</span></tt></a> to pass through.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Also permits <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><code class="xref py py-class docutils literal"><span class="pre">NamedStream</span></code></a> to pass through.</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.util.openany">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">openany</tt><big>(</big><em>directory</em><span class="optional">[</span>, <em>mode='r'</em><span class="optional">]</span><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#openany"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.openany" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">openany</code><span class="sig-paren">(</span><em>directory</em><span class="optional">[</span>, <em>mode='r'</em><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#openany"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.openany" title="Permalink to this definition">¶</a></dt>
 <dd><p>Context manager to open a compressed (bzip2, gzip) or plain file
-(uses <a class="reference internal" href="#MDAnalysis.lib.util.anyopen" title="MDAnalysis.lib.util.anyopen"><tt class="xref py py-func docutils literal"><span class="pre">anyopen()</span></tt></a>).</p>
+(uses <a class="reference internal" href="#MDAnalysis.lib.util.anyopen" title="MDAnalysis.lib.util.anyopen"><code class="xref py py-func docutils literal"><span class="pre">anyopen()</span></code></a>).</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.util.anyopen">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">anyopen</tt><big>(</big><em>datasource</em>, <em>mode='r'</em>, <em>reset=True</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#anyopen"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.anyopen" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">anyopen</code><span class="sig-paren">(</span><em>datasource</em>, <em>mode='r'</em>, <em>reset=True</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#anyopen"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.anyopen" title="Permalink to this definition">¶</a></dt>
 <dd><p>Open datasource (gzipped, bzipped, uncompressed) and return a stream.</p>
-<p><em>datasource</em> can be a filename or a stream (see <a class="reference internal" href="#MDAnalysis.lib.util.isstream" title="MDAnalysis.lib.util.isstream"><tt class="xref py py-func docutils literal"><span class="pre">isstream()</span></tt></a>). By
+<p><em>datasource</em> can be a filename or a stream (see <a class="reference internal" href="#MDAnalysis.lib.util.isstream" title="MDAnalysis.lib.util.isstream"><code class="xref py py-func docutils literal"><span class="pre">isstream()</span></code></a>). By
 default, a stream is reset to its start if possible (via
-<a class="reference external" href="http://docs.python.org/library/io.html#io.IOBase.seek" title="(in Python v2.7)"><tt class="xref py py-meth docutils literal"><span class="pre">seek()</span></tt></a> or <tt class="xref py py-meth docutils literal"><span class="pre">reset()</span></tt>).</p>
-<p>If possible, the attribute <tt class="docutils literal"><span class="pre">stream.name</span></tt> is set to the filename or
+<a class="reference external" href="http://docs.python.org/library/io.html#io.IOBase.seek" title="(in Python v2.7)"><code class="xref py py-meth docutils literal"><span class="pre">seek()</span></code></a> or <code class="xref py py-meth docutils literal"><span class="pre">reset()</span></code>).</p>
+<p>If possible, the attribute <code class="docutils literal"><span class="pre">stream.name</span></code> is set to the filename or
 &#8220;&lt;stream&gt;&#8221; if no filename could be associated with the <em>datasource</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>datasource</em></dt>
-<dd><p class="first last">a file (from <tt class="xref py py-class docutils literal"><span class="pre">file</span></tt> or <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">open()</span></tt></a>) or a stream (e.g. from
-<a class="reference external" href="http://docs.python.org/library/urllib2.html#urllib2.urlopen" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">urllib2.urlopen()</span></tt></a> or <tt class="xref py py-class docutils literal"><span class="pre">cStringIO.StringIO</span></tt>)</p>
+<dd><p class="first last">a file (from <code class="xref py py-class docutils literal"><span class="pre">file</span></code> or <a class="reference external" href="http://docs.python.org/library/functions.html#open" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">open()</span></code></a>) or a stream (e.g. from
+<a class="reference external" href="http://docs.python.org/library/urllib2.html#urllib2.urlopen" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">urllib2.urlopen()</span></code></a> or <code class="xref py py-class docutils literal"><span class="pre">cStringIO.StringIO</span></code>)</p>
 </dd>
 <dt><em>mode</em></dt>
 <dd><p class="first last">&#8216;r&#8217; or &#8216;w&#8217; or &#8216;a&#8217;, more complicated modes (&#8216;r+&#8217;, &#8216;w+&#8217; are not supported because
-only the first letter is looked at) [<tt class="docutils literal"><span class="pre">'r'</span></tt>]</p>
+only the first letter is looked at) [<code class="docutils literal"><span class="pre">'r'</span></code>]</p>
 </dd>
 <dt><em>reset</em></dt>
-<dd><p class="first last">try to read (<em>mode</em> &#8216;r&#8217;) the stream from the start [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">try to read (<em>mode</em> &#8216;r&#8217;) the stream from the start [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">tuple <tt class="docutils literal"><span class="pre">stream</span></tt> which is a file-like object</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">tuple <code class="docutils literal"><span class="pre">stream</span></code> which is a file-like object</p>
 </td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.lib.util.openany" title="MDAnalysis.lib.util.openany"><tt class="xref py py-func docutils literal"><span class="pre">openany()</span></tt></a> to be used with the <a class="reference external" href="http://docs.python.org/reference/compound_stmts.html#with" title="(in Python v2.7)"><tt class="xref std std-keyword docutils literal"><span class="pre">with</span></tt></a> statement.</p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.lib.util.openany" title="MDAnalysis.lib.util.openany"><code class="xref py py-func docutils literal"><span class="pre">openany()</span></code></a> to be used with the <a class="reference external" href="http://docs.python.org/reference/compound_stmts.html#with" title="(in Python v2.7)"><code class="xref std std-keyword docutils literal"><span class="pre">with</span></code></a> statement.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Only returns the <code class="docutils literal"><span class="pre">stream</span></code> and tries to set <code class="docutils literal"><span class="pre">stream.name</span> <span class="pre">=</span> <span class="pre">filename</span></code> instead of the previous
+behavior to return a tuple <code class="docutils literal"><span class="pre">(stream,</span> <span class="pre">filename)</span></code>.</p>
 </div>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Only returns the <tt class="docutils literal"><span class="pre">stream</span></tt> and tries to set <tt class="docutils literal"><span class="pre">stream.name</span> <span class="pre">=</span> <span class="pre">filename</span></tt> instead of the previous
-behavior to return a tuple <tt class="docutils literal"><span class="pre">(stream,</span> <span class="pre">filename)</span></tt>.</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.util.greedy_splitext">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">greedy_splitext</tt><big>(</big><em>p</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#greedy_splitext"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.greedy_splitext" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">greedy_splitext</code><span class="sig-paren">(</span><em>p</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#greedy_splitext"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.greedy_splitext" title="Permalink to this definition">¶</a></dt>
 <dd><p>Split extension in path <em>p</em> at the left-most separator.</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.util.which">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">which</tt><big>(</big><em>program</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#which"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.which" title="Permalink to this definition">¶</a></dt>
-<dd><p>Determine full path of executable <em>program</em> on <span class="target" id="index-0"></span><a class="reference external" href="http://matplotlib.org/faq/environment_variables_faq.html#envvar-PATH" title="(in Matplotlib v1.4.3)"><tt class="xref std std-envvar docutils literal"><span class="pre">PATH</span></tt></a>.</p>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">which</code><span class="sig-paren">(</span><em>program</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#which"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.which" title="Permalink to this definition">¶</a></dt>
+<dd><p>Determine full path of executable <em>program</em> on <span class="target" id="index-0"></span><a class="reference external" href="http://matplotlib.org/faq/environment_variables_faq.html#envvar-PATH" title="(in Matplotlib v1.4.3)"><code class="xref std std-envvar docutils literal"><span class="pre">PATH</span></code></a>.</p>
 <p>(Jay at <a class="reference external" href="http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python">http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python</a>)</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.util.realpath">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">realpath</tt><big>(</big><em>*args</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#realpath"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.realpath" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">realpath</code><span class="sig-paren">(</span><em>*args</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#realpath"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.realpath" title="Permalink to this definition">¶</a></dt>
 <dd><p>Join all args and return the real path, rooted at /.</p>
 <p>Expands &#8216;~&#8217;, &#8216;~user&#8217;, and environment variables such as :envvar`$HOME`.</p>
-<p>Returns <tt class="docutils literal"><span class="pre">None</span></tt> if any of the args is <tt class="docutils literal"><span class="pre">None</span></tt>.</p>
+<p>Returns <code class="docutils literal"><span class="pre">None</span></code> if any of the args is <code class="docutils literal"><span class="pre">None</span></code>.</p>
+</dd></dl>
+
+<dl class="function">
+<dt id="MDAnalysis.lib.util.guess_format">
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">guess_format</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#guess_format"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.guess_format" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return the format of <em>filename</em></p>
+<p>The current heuristic simply looks at the filename extension
+and can work around compressed format extensions</p>
+<p><em>filename</em> can also be a stream, in which case
+<em>filename.name</em> is looked at for a hint to the format</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><em>ValueError</em></td>
+</tr>
+</tbody>
+</table>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0: </span>Moved into lib.util</p>
+</div>
 </dd></dl>
 
 </div>
@@ -218,14 +241,14 @@ <h2>9.9.1. Files and directories<a class="headerlink" href="#files-and-directori
 <h2>9.9.2. Streams<a class="headerlink" href="#streams" title="Permalink to this headline">¶</a></h2>
 <p>Many of the readers are not restricted to just reading files. They can
 also use gzip-compressed or bzip2-compressed files (through the
-internal use of <a class="reference internal" href="#MDAnalysis.lib.util.openany" title="MDAnalysis.lib.util.openany"><tt class="xref py py-func docutils literal"><span class="pre">openany()</span></tt></a>). It is also possible to provide more
-general streams as inputs, such as a <a class="reference external" href="http://docs.python.org/library/stringio.html#cStringIO.StringIO" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">cStringIO.StringIO()</span></tt></a>
+internal use of <a class="reference internal" href="#MDAnalysis.lib.util.openany" title="MDAnalysis.lib.util.openany"><code class="xref py py-func docutils literal"><span class="pre">openany()</span></code></a>). It is also possible to provide more
+general streams as inputs, such as a <a class="reference external" href="http://docs.python.org/library/stringio.html#cStringIO.StringIO" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">cStringIO.StringIO()</span></code></a>
 instances (essentially, a memory buffer) by wrapping these instances
-into a <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><tt class="xref py py-class docutils literal"><span class="pre">NamedStream</span></tt></a>. This <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><tt class="xref py py-class docutils literal"><span class="pre">NamedStream</span></tt></a> can then be
+into a <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><code class="xref py py-class docutils literal"><span class="pre">NamedStream</span></code></a>. This <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><code class="xref py py-class docutils literal"><span class="pre">NamedStream</span></code></a> can then be
 used in place of an ordinary file name (typically, with a
 class:<cite>~MDAnalysis.core.AtomGroup.Universe</cite> but it is also possible to
-<em>write</em> to such a stream using <tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></tt>).</p>
-<p>In the following example, we use a PDB stored as a string <tt class="docutils literal"><span class="pre">pdb_s</span></tt>:</p>
+<em>write</em> to such a stream using <code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.Writer()</span></code>).</p>
+<p>In the following example, we use a PDB stored as a string <code class="docutils literal"><span class="pre">pdb_s</span></code>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">MDAnalysis</span>
 <span class="kn">from</span> <span class="nn">MDAnalysis.lib.util</span> <span class="kn">import</span> <span class="n">NamedStream</span>
 <span class="kn">import</span> <span class="nn">cStringIO</span>
@@ -239,33 +262,33 @@ <h2>9.9.2. Streams<a class="headerlink" href="#streams" title="Permalink to this
 </pre></div>
 </div>
 <p>It is important to provide a proper pseudo file name with the correct extension
-(&#8221;.pdb&#8221;) to <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><tt class="xref py py-class docutils literal"><span class="pre">NamedStream</span></tt></a> because the file type recognition uses the
+(&#8221;.pdb&#8221;) to <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><code class="xref py py-class docutils literal"><span class="pre">NamedStream</span></code></a> because the file type recognition uses the
 extension of the file name to determine the file format or alternatively
-provide the <tt class="docutils literal"><span class="pre">format=&quot;pdb&quot;</span></tt> keyword argument to the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>.</p>
+provide the <code class="docutils literal"><span class="pre">format=&quot;pdb&quot;</span></code> keyword argument to the
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>.</p>
 <p>The use of streams becomes more interesting when MDAnalysis is used as glue
 between different analysis packages and when one can arrange things so that
 intermediate frames (typically in the PDB format) are not written to disk but
-remain in memory via e.g. <a class="reference external" href="http://docs.python.org/library/stringio.html#module-cStringIO" title="(in Python v2.7)"><tt class="xref py py-mod docutils literal"><span class="pre">cStringIO</span></tt></a> buffers.</p>
+remain in memory via e.g. <a class="reference external" href="http://docs.python.org/library/stringio.html#module-cStringIO" title="(in Python v2.7)"><code class="xref py py-mod docutils literal"><span class="pre">cStringIO</span></code></a> buffers.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">A remote connection created by <a class="reference external" href="http://docs.python.org/library/urllib2.html#urllib2.urlopen" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">urllib2.urlopen()</span></tt></a> is not seekable
+<p class="last">A remote connection created by <a class="reference external" href="http://docs.python.org/library/urllib2.html#urllib2.urlopen" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">urllib2.urlopen()</span></code></a> is not seekable
 and therefore will often not work as an input. But try it...</p>
 </div>
 <dl class="class">
 <dt id="MDAnalysis.lib.util.NamedStream">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">NamedStream</tt><big>(</big><em>stream</em>, <em>filename</em>, <em>reset=True</em>, <em>close=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">NamedStream</code><span class="sig-paren">(</span><em>stream</em>, <em>filename</em>, <em>reset=True</em>, <em>close=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream" title="Permalink to this definition">¶</a></dt>
 <dd><p>Stream that also provides a (fake) name.</p>
 <p>By wrapping a stream <em>stream</em> in this class, it can be passed to
 code that uses inspection of the filename to make decisions. For
-instance. <a class="reference external" href="http://docs.python.org/library/os.path.html#os.path.split" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">os.path.split()</span></tt></a> will work correctly on a
-<a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><tt class="xref py py-class docutils literal"><span class="pre">NamedStream</span></tt></a>.</p>
+instance. <a class="reference external" href="http://docs.python.org/library/os.path.html#os.path.split" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">os.path.split()</span></code></a> will work correctly on a
+<a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><code class="xref py py-class docutils literal"><span class="pre">NamedStream</span></code></a>.</p>
 <p>The class can be used as a context manager.</p>
-<p><a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><tt class="xref py py-class docutils literal"><span class="pre">NamedStream</span></tt></a> is derived from <a class="reference external" href="http://docs.python.org/library/io.html#io.IOBase" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">io.IOBase</span></tt></a> (to indicate that
-it is a stream) <em>and</em> <tt class="xref py py-class docutils literal"><span class="pre">basestring</span></tt> (that one can use
-<a class="reference internal" href="#MDAnalysis.lib.util.iterable" title="MDAnalysis.lib.util.iterable"><tt class="xref py py-func docutils literal"><span class="pre">iterable()</span></tt></a> in the same way as for strings).</p>
+<p><a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><code class="xref py py-class docutils literal"><span class="pre">NamedStream</span></code></a> is derived from <a class="reference external" href="http://docs.python.org/library/io.html#io.IOBase" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">io.IOBase</span></code></a> (to indicate that
+it is a stream) <em>and</em> <code class="xref py py-class docutils literal"><span class="pre">basestring</span></code> (that one can use
+<a class="reference internal" href="#MDAnalysis.lib.util.iterable" title="MDAnalysis.lib.util.iterable"><code class="xref py py-func docutils literal"><span class="pre">iterable()</span></code></a> in the same way as for strings).</p>
 <p class="rubric">Example</p>
-<p>Wrap a <a class="reference external" href="http://docs.python.org/library/stringio.html#cStringIO.StringIO" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">cStringIO.StringIO()</span></tt></a> instance to write to:</p>
+<p>Wrap a <a class="reference external" href="http://docs.python.org/library/stringio.html#cStringIO.StringIO" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">cStringIO.StringIO()</span></code></a> instance to write to:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">cStringIO</span>
 <span class="kn">import</span> <span class="nn">os.path</span>
 <span class="n">stream</span> <span class="o">=</span> <span class="n">cStringIO</span><span class="o">.</span><span class="n">StringIO</span><span class="p">()</span>
@@ -273,13 +296,13 @@ <h2>9.9.2. Streams<a class="headerlink" href="#streams" title="Permalink to this
 <span class="k">print</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">f</span><span class="p">))</span>
 </pre></div>
 </div>
-<p>Wrap a <tt class="xref py py-class docutils literal"><span class="pre">file</span></tt> instance to read from:</p>
+<p>Wrap a <code class="xref py py-class docutils literal"><span class="pre">file</span></code> instance to read from:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">stream</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">&quot;input.pdb&quot;</span><span class="p">)</span>
 <span class="n">f</span> <span class="o">=</span> <span class="n">NamedStream</span><span class="p">(</span><span class="n">stream</span><span class="p">,</span> <span class="n">stream</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
 </pre></div>
 </div>
 <p>Use as a context manager (closes stream automatically when the
-<a class="reference external" href="http://docs.python.org/reference/compound_stmts.html#with" title="(in Python v2.7)"><tt class="xref std std-keyword docutils literal"><span class="pre">with</span></tt></a> block is left):</p>
+<a class="reference external" href="http://docs.python.org/reference/compound_stmts.html#with" title="(in Python v2.7)"><code class="xref std std-keyword docutils literal"><span class="pre">with</span></code></a> block is left):</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="k">with</span> <span class="n">NamedStream</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s">&quot;input.pdb&quot;</span><span class="p">),</span> <span class="s">&quot;input.pdb&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
    <span class="c"># use f</span>
    <span class="k">print</span> <span class="n">f</span><span class="o">.</span><span class="n">closed</span>  <span class="c"># --&gt; False</span>
@@ -289,34 +312,34 @@ <h2>9.9.2. Streams<a class="headerlink" href="#streams" title="Permalink to this
 </div>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">This class uses its own <tt class="xref py py-meth docutils literal"><span class="pre">__getitem__()</span></tt> method so if <em>stream</em>
-implements <tt class="xref py py-meth docutils literal"><span class="pre">stream.__getitem__()</span></tt> then that will be masked and this
+<p class="last">This class uses its own <code class="xref py py-meth docutils literal"><span class="pre">__getitem__()</span></code> method so if <em>stream</em>
+implements <code class="xref py py-meth docutils literal"><span class="pre">stream.__getitem__()</span></code> then that will be masked and this
 class should not be used.</p>
 </div>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
-<p class="last">By default, <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><tt class="xref py py-meth docutils literal"><span class="pre">NamedStream.close()</span></tt></a> will <strong>not close the
-stream</strong> but instead <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.reset" title="MDAnalysis.lib.util.NamedStream.reset"><tt class="xref py py-meth docutils literal"><span class="pre">reset()</span></tt></a> it to the
-beginning. <a class="footnote-reference" href="#namedstreamclose" id="id1">[1]</a> Provide the <tt class="docutils literal"><span class="pre">force=True</span></tt> keyword
-to <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><tt class="xref py py-meth docutils literal"><span class="pre">NamedStream.close()</span></tt></a> to always close the stream.</p>
+<p class="last">By default, <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><code class="xref py py-meth docutils literal"><span class="pre">NamedStream.close()</span></code></a> will <strong>not close the
+stream</strong> but instead <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.reset" title="MDAnalysis.lib.util.NamedStream.reset"><code class="xref py py-meth docutils literal"><span class="pre">reset()</span></code></a> it to the
+beginning. <a class="footnote-reference" href="#namedstreamclose" id="id1">[1]</a> Provide the <code class="docutils literal"><span class="pre">force=True</span></code> keyword
+to <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><code class="xref py py-meth docutils literal"><span class="pre">NamedStream.close()</span></code></a> to always close the stream.</p>
 </div>
-<p>Initialize the <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><tt class="xref py py-class docutils literal"><span class="pre">NamedStream</span></tt></a> from a <em>stream</em> and give it a <em>name</em>.</p>
+<p>Initialize the <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><code class="xref py py-class docutils literal"><span class="pre">NamedStream</span></code></a> from a <em>stream</em> and give it a <em>name</em>.</p>
 <p>The constructor attempts to rewind the stream to the beginning unless
-the keyword <em>reset</em> is set to <tt class="docutils literal"><span class="pre">False</span></tt>. If rewinding fails, a
-<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.StreamWarning</span></tt> is issued.</p>
+the keyword <em>reset</em> is set to <code class="docutils literal"><span class="pre">False</span></code>. If rewinding fails, a
+<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.StreamWarning</span></code> is issued.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">By default, this stream will <em>not</em> be closed by <a class="reference external" href="http://docs.python.org/reference/compound_stmts.html#with" title="(in Python v2.7)"><tt class="xref std std-keyword docutils literal"><span class="pre">with</span></tt></a> and
-<a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><tt class="xref py py-meth docutils literal"><span class="pre">close()</span></tt></a> (see there) unless the <em>close</em> keyword is set to
-<tt class="docutils literal"><span class="pre">True</span></tt>.</p>
+<p class="last">By default, this stream will <em>not</em> be closed by <a class="reference external" href="http://docs.python.org/reference/compound_stmts.html#with" title="(in Python v2.7)"><code class="xref std std-keyword docutils literal"><span class="pre">with</span></code></a> and
+<a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><code class="xref py py-meth docutils literal"><span class="pre">close()</span></code></a> (see there) unless the <em>close</em> keyword is set to
+<code class="docutils literal"><span class="pre">True</span></code>.</p>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>stream</em></dt>
-<dd><p class="first last">open stream (e.g. <tt class="xref py py-class docutils literal"><span class="pre">file</span></tt> or <a class="reference external" href="http://docs.python.org/library/stringio.html#cStringIO.StringIO" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">cStringIO.StringIO()</span></tt></a>)</p>
+<dd><p class="first last">open stream (e.g. <code class="xref py py-class docutils literal"><span class="pre">file</span></code> or <a class="reference external" href="http://docs.python.org/library/stringio.html#cStringIO.StringIO" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">cStringIO.StringIO()</span></code></a>)</p>
 </dd>
 <dt><em>filename</em></dt>
 <dd><p class="first last">the filename that should be associated with the stream</p>
@@ -324,92 +347,93 @@ <h2>9.9.2. Streams<a class="headerlink" href="#streams" title="Permalink to this
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>reset</em></dt>
-<dd><p class="first last">start the stream from the beginning (either <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.reset" title="MDAnalysis.lib.util.NamedStream.reset"><tt class="xref py py-meth docutils literal"><span class="pre">reset()</span></tt></a> or <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.seek" title="MDAnalysis.lib.util.NamedStream.seek"><tt class="xref py py-meth docutils literal"><span class="pre">seek()</span></tt></a>)
-when the class instance is constructed [<tt class="docutils literal"><span class="pre">True</span></tt>]</p>
+<dd><p class="first last">start the stream from the beginning (either <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.reset" title="MDAnalysis.lib.util.NamedStream.reset"><code class="xref py py-meth docutils literal"><span class="pre">reset()</span></code></a> or <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.seek" title="MDAnalysis.lib.util.NamedStream.seek"><code class="xref py py-meth docutils literal"><span class="pre">seek()</span></code></a>)
+when the class instance is constructed [<code class="docutils literal"><span class="pre">True</span></code>]</p>
 </dd>
 <dt><em>close</em></dt>
-<dd><p class="first last">close the stream when a <a class="reference external" href="http://docs.python.org/reference/compound_stmts.html#with" title="(in Python v2.7)"><tt class="xref std std-keyword docutils literal"><span class="pre">with</span></tt></a> block exits or when
-<a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><tt class="xref py py-meth docutils literal"><span class="pre">close()</span></tt></a> is called; note that the default is <strong>not to close
-the stream</strong> [<tt class="docutils literal"><span class="pre">False</span></tt>]</p>
+<dd><p class="first last">close the stream when a <a class="reference external" href="http://docs.python.org/reference/compound_stmts.html#with" title="(in Python v2.7)"><code class="xref std std-keyword docutils literal"><span class="pre">with</span></code></a> block exits or when
+<a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><code class="xref py py-meth docutils literal"><span class="pre">close()</span></code></a> is called; note that the default is <strong>not to close
+the stream</strong> [<code class="docutils literal"><span class="pre">False</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.lib.util.NamedStream.close">
-<tt class="descname">close</tt><big>(</big><em>force=False</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><em>force=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reset or close the stream.</p>
-<p>If <tt class="xref py py-attr docutils literal"><span class="pre">NamedStream.close_stream</span></tt> is set to <tt class="docutils literal"><span class="pre">False</span></tt> (the default)
-then this method will <em>not close the stream</em> and only <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.reset" title="MDAnalysis.lib.util.NamedStream.reset"><tt class="xref py py-meth docutils literal"><span class="pre">reset()</span></tt></a> it.</p>
-<p>If the <em>force</em> = <tt class="docutils literal"><span class="pre">True</span></tt> keyword is provided, the stream will be
+<p>If <code class="xref py py-attr docutils literal"><span class="pre">NamedStream.close_stream</span></code> is set to <code class="docutils literal"><span class="pre">False</span></code> (the default)
+then this method will <em>not close the stream</em> and only <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.reset" title="MDAnalysis.lib.util.NamedStream.reset"><code class="xref py py-meth docutils literal"><span class="pre">reset()</span></code></a> it.</p>
+<p>If the <em>force</em> = <code class="docutils literal"><span class="pre">True</span></code> keyword is provided, the stream will be
 closed.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">This <tt class="docutils literal"><span class="pre">close()</span></tt> method is non-standard. <tt class="docutils literal"><span class="pre">del</span> <span class="pre">NamedStream</span></tt>
+<p class="last">This <code class="docutils literal"><span class="pre">close()</span></code> method is non-standard. <code class="docutils literal"><span class="pre">del</span> <span class="pre">NamedStream</span></code>
 always closes the underlying stream.</p>
 </div>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.lib.util.NamedStream.closed">
-<tt class="descname">closed</tt><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.closed"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.closed" title="Permalink to this definition">¶</a></dt>
-<dd><p><tt class="docutils literal"><span class="pre">True</span></tt> if stream is closed.</p>
+<code class="descname">closed</code><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.closed" title="Permalink to this definition">¶</a></dt>
+<dd><p><code class="docutils literal"><span class="pre">True</span></code> if stream is closed.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.util.NamedStream.fileno">
-<tt class="descname">fileno</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.fileno"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.fileno" title="Permalink to this definition">¶</a></dt>
+<code class="descname">fileno</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.fileno"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.fileno" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return the underlying file descriptor (an integer) of the stream if it exists.</p>
-<p>An <tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> is raised if the IO object does not use a file descriptor.</p>
+<p>An <code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> is raised if the IO object does not use a file descriptor.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.util.NamedStream.flush">
-<tt class="descname">flush</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.flush"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.flush" title="Permalink to this definition">¶</a></dt>
+<code class="descname">flush</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.flush"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.flush" title="Permalink to this definition">¶</a></dt>
 <dd><p>Flush the write buffers of the stream if applicable.</p>
 <p>This does nothing for read-only and non-blocking streams. For file
-objects one also needs to call <a class="reference external" href="http://docs.python.org/library/os.html#os.fsync" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">os.fsync()</span></tt></a> to write contents to
+objects one also needs to call <a class="reference external" href="http://docs.python.org/library/os.html#os.fsync" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">os.fsync()</span></code></a> to write contents to
 disk.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.util.NamedStream.readable">
-<tt class="descname">readable</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.readable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.readable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Return <tt class="docutils literal"><span class="pre">True</span></tt> if the stream can be read from.</p>
-<p>If <tt class="docutils literal"><span class="pre">False</span></tt>, <tt class="xref py py-meth docutils literal"><span class="pre">read()</span></tt> will raise <tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt>.</p>
+<code class="descname">readable</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.readable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.readable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return <code class="docutils literal"><span class="pre">True</span></code> if the stream can be read from.</p>
+<p>If <code class="docutils literal"><span class="pre">False</span></code>, <code class="xref py py-meth docutils literal"><span class="pre">read()</span></code> will raise <code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.util.NamedStream.reset">
-<tt class="descname">reset</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.reset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.reset" title="Permalink to this definition">¶</a></dt>
+<code class="descname">reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.reset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.reset" title="Permalink to this definition">¶</a></dt>
 <dd><p>Move to the beginning of the stream</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.util.NamedStream.seek">
-<tt class="descname">seek</tt><big>(</big><em>offset</em>, <em>whence=0</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.seek"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.seek" title="Permalink to this definition">¶</a></dt>
+<code class="descname">seek</code><span class="sig-paren">(</span><em>offset</em>, <em>whence=0</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.seek"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.seek" title="Permalink to this definition">¶</a></dt>
 <dd><p>Change the stream position to the given byte <em>offset</em> .</p>
 <p><em>offset</em> is interpreted relative to the position indicated by
 <em>whence</em>. Values for <em>whence</em> are:</p>
 <ul class="simple">
-<li><tt class="xref py py-data docutils literal"><span class="pre">io.SEEK_SET</span></tt> or 0 – start of the stream (the default); <em>offset</em>
+<li><code class="xref py py-data docutils literal"><span class="pre">io.SEEK_SET</span></code> or 0 – start of the stream (the default); <em>offset</em>
 should be zero or positive</li>
-<li><tt class="xref py py-data docutils literal"><span class="pre">io.SEEK_CUR</span></tt> or 1 – current stream position; <em>offset</em> may be
+<li><code class="xref py py-data docutils literal"><span class="pre">io.SEEK_CUR</span></code> or 1 – current stream position; <em>offset</em> may be
 negative</li>
-<li><tt class="xref py py-data docutils literal"><span class="pre">io.SEEK_END</span></tt> or 2 – end of the stream; <em>offset</em> is usually
+<li><code class="xref py py-data docutils literal"><span class="pre">io.SEEK_END</span></code> or 2 – end of the stream; <em>offset</em> is usually
 negative</li>
 </ul>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">the new absolute position.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">the new absolute position.</td>
 </tr>
 </tbody>
 </table>
@@ -417,20 +441,20 @@ <h2>9.9.2. Streams<a class="headerlink" href="#streams" title="Permalink to this
 
 <dl class="method">
 <dt id="MDAnalysis.lib.util.NamedStream.seekable">
-<tt class="descname">seekable</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.seekable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.seekable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Return <tt class="docutils literal"><span class="pre">True</span></tt> if the stream supports random access.</p>
-<p>If <tt class="docutils literal"><span class="pre">False</span></tt>, <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.seek" title="MDAnalysis.lib.util.NamedStream.seek"><tt class="xref py py-meth docutils literal"><span class="pre">seek()</span></tt></a>, <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.tell" title="MDAnalysis.lib.util.NamedStream.tell"><tt class="xref py py-meth docutils literal"><span class="pre">tell()</span></tt></a> and <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.truncate" title="MDAnalysis.lib.util.NamedStream.truncate"><tt class="xref py py-meth docutils literal"><span class="pre">truncate()</span></tt></a> will raise <tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt>.</p>
+<code class="descname">seekable</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.seekable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.seekable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return <code class="docutils literal"><span class="pre">True</span></code> if the stream supports random access.</p>
+<p>If <code class="docutils literal"><span class="pre">False</span></code>, <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.seek" title="MDAnalysis.lib.util.NamedStream.seek"><code class="xref py py-meth docutils literal"><span class="pre">seek()</span></code></a>, <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.tell" title="MDAnalysis.lib.util.NamedStream.tell"><code class="xref py py-meth docutils literal"><span class="pre">tell()</span></code></a> and <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.truncate" title="MDAnalysis.lib.util.NamedStream.truncate"><code class="xref py py-meth docutils literal"><span class="pre">truncate()</span></code></a> will raise <code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.util.NamedStream.tell">
-<tt class="descname">tell</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.tell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.tell" title="Permalink to this definition">¶</a></dt>
+<code class="descname">tell</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.tell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.tell" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return the current stream position.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.util.NamedStream.truncate">
-<tt class="descname">truncate</tt><big>(</big><em>*size</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.truncate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.truncate" title="Permalink to this definition">¶</a></dt>
+<code class="descname">truncate</code><span class="sig-paren">(</span><em>*size</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.truncate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.truncate" title="Permalink to this definition">¶</a></dt>
 <dd><p>Truncate the stream&#8217;s size to <em>size</em>.</p>
 <p>The size defaults to the current position (if no <em>size</em> argument is
 supplied). The current file position is not changed.</p>
@@ -438,48 +462,49 @@ <h2>9.9.2. Streams<a class="headerlink" href="#streams" title="Permalink to this
 
 <dl class="method">
 <dt id="MDAnalysis.lib.util.NamedStream.writable">
-<tt class="descname">writable</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.writable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.writable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Return <tt class="docutils literal"><span class="pre">True</span></tt> if the stream can be written to.</p>
-<p>If <tt class="docutils literal"><span class="pre">False</span></tt>, <tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt> will raise <tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt>.</p>
+<code class="descname">writable</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#NamedStream.writable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.NamedStream.writable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return <code class="docutils literal"><span class="pre">True</span></code> if the stream can be written to.</p>
+<p>If <code class="docutils literal"><span class="pre">False</span></code>, <code class="xref py py-meth docutils literal"><span class="pre">write()</span></code> will raise <code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code>.</p>
 </dd></dl>
 
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.util.isstream">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">isstream</tt><big>(</big><em>obj</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#isstream"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.isstream" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">isstream</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#isstream"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.isstream" title="Permalink to this definition">¶</a></dt>
 <dd><p>Detect if <em>obj</em> is a stream.</p>
 <p>We consider anything a stream that has the methods</p>
 <ul class="simple">
-<li><tt class="docutils literal"><span class="pre">close()</span></tt></li>
+<li><code class="docutils literal"><span class="pre">close()</span></code></li>
 </ul>
 <p>and either set of the following</p>
 <ul class="simple">
-<li><tt class="docutils literal"><span class="pre">read()</span></tt>, <tt class="docutils literal"><span class="pre">readline()</span></tt>, <tt class="docutils literal"><span class="pre">readlines()</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">write()</span></tt>, <tt class="docutils literal"><span class="pre">writeline()</span></tt>, <tt class="docutils literal"><span class="pre">writelines()</span></tt></li>
+<li><code class="docutils literal"><span class="pre">read()</span></code>, <code class="docutils literal"><span class="pre">readline()</span></code>, <code class="docutils literal"><span class="pre">readlines()</span></code></li>
+<li><code class="docutils literal"><span class="pre">write()</span></code>, <code class="docutils literal"><span class="pre">writeline()</span></code>, <code class="docutils literal"><span class="pre">writelines()</span></code></li>
 </ul>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference external" href="http://docs.python.org/library/io.html#module-io" title="(in Python v2.7)"><tt class="xref py py-mod docutils literal"><span class="pre">io</span></tt></a></p>
+<p class="last"><a class="reference external" href="http://docs.python.org/library/io.html#module-io" title="(in Python v2.7)"><code class="xref py py-mod docutils literal"><span class="pre">io</span></code></a></p>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>obj</em></dt>
 <dd><p class="first last">stream or string</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><tt class="docutils literal"><span class="pre">True</span></tt> is <em>obj</em> is a stream, <tt class="docutils literal"><span class="pre">False</span></tt> otherwise</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="docutils literal"><span class="pre">True</span></code> is <em>obj</em> is a stream, <code class="docutils literal"><span class="pre">False</span></code> otherwise</p>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
 </dd></dl>
 
 </div>
@@ -487,20 +512,20 @@ <h2>9.9.2. Streams<a class="headerlink" href="#streams" title="Permalink to this
 <h2>9.9.3. Containers and lists<a class="headerlink" href="#containers-and-lists" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.lib.util.iterable">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">iterable</tt><big>(</big><em>obj</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#iterable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.iterable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns <tt class="docutils literal"><span class="pre">True</span></tt> if <em>obj</em> can be iterated over and is <em>not</em> a  string.</p>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">iterable</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#iterable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.iterable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns <code class="docutils literal"><span class="pre">True</span></code> if <em>obj</em> can be iterated over and is <em>not</em> a  string.</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.util.asiterable">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">asiterable</tt><big>(</big><em>obj</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#asiterable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.asiterable" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">asiterable</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#asiterable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.asiterable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns obj so that it can be iterated over; a string is <em>not</em> treated as iterable</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.util.hasmethod">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">hasmethod</tt><big>(</big><em>obj</em>, <em>m</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#hasmethod"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.hasmethod" title="Permalink to this definition">¶</a></dt>
-<dd><p>Return <tt class="docutils literal"><span class="pre">True</span></tt> if object <em>obj</em> contains the method <em>m</em>.</p>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">hasmethod</code><span class="sig-paren">(</span><em>obj</em>, <em>m</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#hasmethod"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.hasmethod" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return <code class="docutils literal"><span class="pre">True</span></code> if object <em>obj</em> contains the method <em>m</em>.</p>
 </dd></dl>
 
 </div>
@@ -508,7 +533,7 @@ <h2>9.9.3. Containers and lists<a class="headerlink" href="#containers-and-lists
 <h2>9.9.4. File parsing<a class="headerlink" href="#file-parsing" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.lib.util.FORTRANReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">FORTRANReader</tt><big>(</big><em>fmt</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#FORTRANReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.FORTRANReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">FORTRANReader</code><span class="sig-paren">(</span><em>fmt</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#FORTRANReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.FORTRANReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>FORTRANReader provides a method to parse FORTRAN formatted lines in a file.</p>
 <p>Usage:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">atomformat</span> <span class="o">=</span> <span class="n">FORTRANReader</span><span class="p">(</span><span class="s">&#39;2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10&#39;</span><span class="p">)</span>
@@ -518,19 +543,19 @@ <h2>9.9.4. File parsing<a class="headerlink" href="#file-parsing" title="Permali
 </div>
 <p>Fortran format edit descriptors; see <a class="reference external" href="http://www.webcitation.org/5xbaWMV2x">Fortran Formats</a> for the syntax.</p>
 <p>Only simple one-character specifiers supported here: <em>I F E A X</em> (see
-<a class="reference internal" href="#MDAnalysis.lib.util.FORTRAN_format_regex" title="MDAnalysis.lib.util.FORTRAN_format_regex"><tt class="xref py py-data docutils literal"><span class="pre">FORTRAN_format_regex</span></tt></a>).</p>
+<a class="reference internal" href="#MDAnalysis.lib.util.FORTRAN_format_regex" title="MDAnalysis.lib.util.FORTRAN_format_regex"><code class="xref py py-data docutils literal"><span class="pre">FORTRAN_format_regex</span></code></a>).</p>
 <p>Strings are stripped of leading and trailing white space.</p>
 <p>Set up the reader with the FORTRAN format string.</p>
 <p>The string <em>fmt</em> should look like &#8216;2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10&#8217;.</p>
 <dl class="method">
 <dt id="MDAnalysis.lib.util.FORTRANReader.number_of_matches">
-<tt class="descname">number_of_matches</tt><big>(</big><em>line</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#FORTRANReader.number_of_matches"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.FORTRANReader.number_of_matches" title="Permalink to this definition">¶</a></dt>
+<code class="descname">number_of_matches</code><span class="sig-paren">(</span><em>line</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#FORTRANReader.number_of_matches"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.FORTRANReader.number_of_matches" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return how many format entries could be populated with legal values.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.lib.util.FORTRANReader.parse_FORTRAN_format">
-<tt class="descname">parse_FORTRAN_format</tt><big>(</big><em>edit_descriptor</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#FORTRANReader.parse_FORTRAN_format"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.FORTRANReader.parse_FORTRAN_format" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse_FORTRAN_format</code><span class="sig-paren">(</span><em>edit_descriptor</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#FORTRANReader.parse_FORTRAN_format"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.FORTRANReader.parse_FORTRAN_format" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse the descriptor.</p>
 <blockquote>
 <div>parse_FORTRAN_format(edit_descriptor) &#8211;&gt; dict</div></blockquote>
@@ -538,10 +563,10 @@ <h2>9.9.4. File parsing<a class="headerlink" href="#file-parsing" title="Permali
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">dict with totallength (in chars), repeat, length,
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">dict with totallength (in chars), repeat, length,
 format, decimals</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> if the <em>edit_descriptor</em> is not recognized
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> if the <em>edit_descriptor</em> is not recognized
 and cannot be parsed</td>
 </tr>
 </tbody>
@@ -556,23 +581,23 @@ <h2>9.9.4. File parsing<a class="headerlink" href="#file-parsing" title="Permali
 
 <dl class="method">
 <dt id="MDAnalysis.lib.util.FORTRANReader.read">
-<tt class="descname">read</tt><big>(</big><em>line</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#FORTRANReader.read"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.FORTRANReader.read" title="Permalink to this definition">¶</a></dt>
+<code class="descname">read</code><span class="sig-paren">(</span><em>line</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#FORTRANReader.read"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.FORTRANReader.read" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse <em>line</em> according to the format string and return list of values.</p>
 <p>Values are converted to Python types according to the format specifier.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">list of entries with appropriate types</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">list of entries with appropriate types</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> if any of the conversions cannot be made
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> if any of the conversions cannot be made
 (e.g. space for an int)</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.lib.util.FORTRANReader.number_of_matches" title="MDAnalysis.lib.util.FORTRANReader.number_of_matches"><tt class="xref py py-meth docutils literal"><span class="pre">FORTRANReader.number_of_matches()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.lib.util.FORTRANReader.number_of_matches" title="MDAnalysis.lib.util.FORTRANReader.number_of_matches"><code class="xref py py-meth docutils literal"><span class="pre">FORTRANReader.number_of_matches()</span></code></a></p>
 </div>
 </dd></dl>
 
@@ -580,9 +605,9 @@ <h2>9.9.4. File parsing<a class="headerlink" href="#file-parsing" title="Permali
 
 <dl class="data">
 <dt id="MDAnalysis.lib.util.FORTRAN_format_regex">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">FORTRAN_format_regex</tt><em class="property"> = '(?P&lt;repeat&gt;\\d+?)(?P&lt;format&gt;[IFEAX])(?P&lt;numfmt&gt;(?P&lt;length&gt;\\d+)(\\.(?P&lt;decimals&gt;\\d+))?)?'</em><a class="headerlink" href="#MDAnalysis.lib.util.FORTRAN_format_regex" title="Permalink to this definition">¶</a></dt>
-<dd><p>Regular expresssion (see <a class="reference external" href="http://docs.python.org/library/re.html#module-re" title="(in Python v2.7)"><tt class="xref py py-mod docutils literal"><span class="pre">re</span></tt></a>) to parse a simple <a class="reference external" href="http://www.cs.mtu.edu/~shene/COURSES/cs201/NOTES/chap05/format.html">FORTRAN edit descriptor</a>.
-<tt class="docutils literal"><span class="pre">(?P&lt;repeat&gt;\d?)(?P&lt;format&gt;[IFELAX])(?P&lt;numfmt&gt;(?P&lt;length&gt;\d+)(\.(?P&lt;decimals&gt;\d+))?)?</span></tt></p>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">FORTRAN_format_regex</code><em class="property"> = '(?P&lt;repeat&gt;\\d+?)(?P&lt;format&gt;[IFEAX])(?P&lt;numfmt&gt;(?P&lt;length&gt;\\d+)(\\.(?P&lt;decimals&gt;\\d+))?)?'</em><a class="headerlink" href="#MDAnalysis.lib.util.FORTRAN_format_regex" title="Permalink to this definition">¶</a></dt>
+<dd><p>Regular expresssion (see <a class="reference external" href="http://docs.python.org/library/re.html#module-re" title="(in Python v2.7)"><code class="xref py py-mod docutils literal"><span class="pre">re</span></code></a>) to parse a simple <a class="reference external" href="http://www.cs.mtu.edu/~shene/COURSES/cs201/NOTES/chap05/format.html">FORTRAN edit descriptor</a>.
+<code class="docutils literal"><span class="pre">(?P&lt;repeat&gt;\d?)(?P&lt;format&gt;[IFELAX])(?P&lt;numfmt&gt;(?P&lt;length&gt;\d+)(\.(?P&lt;decimals&gt;\d+))?)?</span></code></p>
 </dd></dl>
 
 </div>
@@ -590,7 +615,7 @@ <h2>9.9.4. File parsing<a class="headerlink" href="#file-parsing" title="Permali
 <h2>9.9.5. Data manipulation and handling<a class="headerlink" href="#data-manipulation-and-handling" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.lib.util.fixedwidth_bins">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">fixedwidth_bins</tt><big>(</big><em>delta</em>, <em>xmin</em>, <em>xmax</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#fixedwidth_bins"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.fixedwidth_bins" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">fixedwidth_bins</code><span class="sig-paren">(</span><em>delta</em>, <em>xmin</em>, <em>xmax</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#fixedwidth_bins"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.fixedwidth_bins" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return bins of width delta that cover xmin,xmax (or a larger range).</p>
 <p>dict = fixedwidth_bins(delta,xmin,xmax)</p>
 <p>The dict contains &#8216;Nbins&#8217;, &#8216;delta&#8217;, &#8216;min&#8217;, and &#8216;max&#8217;.</p>
@@ -601,17 +626,17 @@ <h2>9.9.5. Data manipulation and handling<a class="headerlink" href="#data-manip
 <h2>9.9.6. Strings<a class="headerlink" href="#strings" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.lib.util.convert_aa_code">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">convert_aa_code</tt><big>(</big><em>x</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#convert_aa_code"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.convert_aa_code" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">convert_aa_code</code><span class="sig-paren">(</span><em>x</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#convert_aa_code"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.convert_aa_code" title="Permalink to this definition">¶</a></dt>
 <dd><p>Converts between 3-letter and 1-letter amino acid codes.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last">Data are defined in <tt class="xref py py-data docutils literal"><span class="pre">amino_acid_codes</span></tt> and <tt class="xref py py-data docutils literal"><span class="pre">inverse_aa_codes</span></tt>.</p>
+<p class="last">Data are defined in <code class="xref py py-data docutils literal"><span class="pre">amino_acid_codes</span></code> and <code class="xref py py-data docutils literal"><span class="pre">inverse_aa_codes</span></code>.</p>
 </div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.lib.util.parse_residue">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">parse_residue</tt><big>(</big><em>residue</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#parse_residue"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.parse_residue" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">parse_residue</code><span class="sig-paren">(</span><em>residue</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#parse_residue"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.parse_residue" title="Permalink to this definition">¶</a></dt>
 <dd><p>Process residue string.</p>
 <dl class="docutils">
 <dt>Examples:</dt>
@@ -628,13 +653,13 @@ <h2>9.9.6. Strings<a class="headerlink" href="#strings" title="Permalink to this
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Argument :</th><td class="field-body">The <em>residue</em> must contain a 1-letter or 3-letter or
+<tr class="field-odd field"><th class="field-name">Argument:</th><td class="field-body">The <em>residue</em> must contain a 1-letter or 3-letter or
 4-letter residue string, a number (the resid) and
 optionally an atom identifier, which must be separate
 from the residue with a colon (&#8221;:&#8221;). White space is
 allowed in between.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><cite>(3-letter aa string, resid, atomname)</cite>; known 1-letter
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><cite>(3-letter aa string, resid, atomname)</cite>; known 1-letter
 aa codes are converted to 3-letter codes</td>
 </tr>
 </tbody>
@@ -643,9 +668,9 @@ <h2>9.9.6. Strings<a class="headerlink" href="#strings" title="Permalink to this
 
 <dl class="function">
 <dt id="MDAnalysis.lib.util.conv_float">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">conv_float</tt><big>(</big><em>s</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#conv_float"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.conv_float" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">conv_float</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#conv_float"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.conv_float" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert an object <em>s</em> to float if possible.</p>
-<p>Function to be passed into <a class="reference external" href="http://docs.python.org/library/functions.html#map" title="(in Python v2.7)"><tt class="xref py py-func docutils literal"><span class="pre">map()</span></tt></a> or a list comprehension. If
+<p>Function to be passed into <a class="reference external" href="http://docs.python.org/library/functions.html#map" title="(in Python v2.7)"><code class="xref py py-func docutils literal"><span class="pre">map()</span></code></a> or a list comprehension. If
 the argument can be interpreted as a float it is converted,
 otherwise the original object is passed back.</p>
 </dd></dl>
@@ -655,44 +680,47 @@ <h2>9.9.6. Strings<a class="headerlink" href="#strings" title="Permalink to this
 <h2>9.9.7. Class decorators<a class="headerlink" href="#class-decorators" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.lib.util.cached">
-<tt class="descclassname">MDAnalysis.lib.util.</tt><tt class="descname">cached</tt><big>(</big><em>key</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#cached"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.cached" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.lib.util.</code><code class="descname">cached</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/lib/util.html#cached"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.lib.util.cached" title="Permalink to this definition">¶</a></dt>
 <dd><p>Cache a property within a class</p>
-<p>Requires the Class to have a cache dict called <tt class="docutils literal"><span class="pre">_cache</span></tt>.</p>
+<p>Requires the Class to have a cache dict called <code class="docutils literal"><span class="pre">_cache</span></code>.</p>
 <p>Usage:</p>
-<div class="highlight-python"><pre>class A(object):
+<div class="highlight-python"><div class="highlight"><pre>class A(object):
     def__init__(self):
         self._cache = dict()
 
     @property
-    @cached('keyname')
+    @cached(&#39;keyname&#39;)
     def size(self):
         # This code gets ran only if the lookup of keyname fails
         # After this code has been ran once, the result is stored in
-        # _cache with the key: 'keyname'
-        size = 10.0</pre>
+        # _cache with the key: &#39;keyname&#39;
+        size = 10.0
+</pre></div>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
 </dd></dl>
 
 <p class="rubric">Footnotes</p>
 <table class="docutils footnote" frame="void" id="namedstreamclose" rules="none">
 <colgroup><col class="label" /><col /></colgroup>
 <tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[1]</a></td><td>The reason why <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><tt class="xref py py-meth docutils literal"><span class="pre">NamedStream.close()</span></tt></a> does
+<tr><td class="label"><a class="fn-backref" href="#id1">[1]</a></td><td>The reason why <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><code class="xref py py-meth docutils literal"><span class="pre">NamedStream.close()</span></code></a> does
 not close a stream by default (but just rewinds it to the
-beginning) is so that one can use the class <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><tt class="xref py py-class docutils literal"><span class="pre">NamedStream</span></tt></a> as
+beginning) is so that one can use the class <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><code class="xref py py-class docutils literal"><span class="pre">NamedStream</span></code></a> as
 a drop-in replacement for file names, which are often re-opened
 (e.g. when the same file is used as a topology and coordinate file
 or when repeatedly iterating through a trajectory in some
-implementations). The <tt class="docutils literal"><span class="pre">close=True</span></tt> keyword can be supplied in
-order to make <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><tt class="xref py py-meth docutils literal"><span class="pre">NamedStream.close()</span></tt></a> actually close the
-underlying stream and <tt class="docutils literal"><span class="pre">NamedStream.close(force=True)</span></tt> will also
+implementations). The <code class="docutils literal"><span class="pre">close=True</span></code> keyword can be supplied in
+order to make <a class="reference internal" href="#MDAnalysis.lib.util.NamedStream.close" title="MDAnalysis.lib.util.NamedStream.close"><code class="xref py py-meth docutils literal"><span class="pre">NamedStream.close()</span></code></a> actually close the
+underlying stream and <code class="docutils literal"><span class="pre">NamedStream.close(force=True)</span></code> will also
 close it.</td></tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Moved mathematical functions into lib.mdamath</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Moved mathematical functions into lib.mdamath</p>
+</div>
 </div>
 </div>
 
@@ -702,7 +730,7 @@ <h2>9.9.7. Class decorators<a class="headerlink" href="#class-decorators" title=
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -712,16 +740,16 @@ <h3>Navigation</h3>
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="../version.html" title="10. Version information for MDAnalysis"
+          <a href="../version.html" title="10. Version information for MDAnalysis — MDAnalysis.version"
              >next</a> |</li>
         <li class="right" >
           <a href="qcprot.html" title="9.8. Fast QCP RMSD structure alignment — MDAnalysis.lib.qcprot"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../lib_modules.html" >9. MDAnalysis library</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -731,7 +759,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/lib_modules.html b/package/doc/html/documentation_pages/lib_modules.html
index 852d04a1c79..48e95e9ce45 100644
--- a/package/doc/html/documentation_pages/lib_modules.html
+++ b/package/doc/html/documentation_pages/lib_modules.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>9. MDAnalysis library &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>9. MDAnalysis library &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="9.1. Fast distance array computation — MDAnalysis.lib.distances" href="lib/distances.html" />
     <link rel="prev" title="8.1.2. 3D Streamplot" href="visualization/streamlines_3D.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -50,10 +48,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="visualization/streamlines_3D.html" title="8.1.2. 3D Streamplot"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../index.html">
               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -63,13 +61,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">8.1.2. 3D Streamplot</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="lib/distances.html"
-                        title="next chapter">9.1. Fast distance array computation &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.lib.distances</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/lib_modules.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">9.1. Fast distance array computation &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.distances</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/lib_modules.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -88,34 +88,38 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="mdanalysis-library">
 <span id="lib"></span><h1>9. MDAnalysis library<a class="headerlink" href="#mdanalysis-library" title="Permalink to this headline">¶</a></h1>
-<p><a class="reference internal" href="lib/distances.html#module-MDAnalysis.lib.distances" title="MDAnalysis.lib.distances"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.distances</span></tt></a> contains many high performance
+<p><a class="reference internal" href="lib/distances.html#module-MDAnalysis.lib.distances" title="MDAnalysis.lib.distances"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.distances</span></code></a> contains many high performance
 maths functions.</p>
-<p><a class="reference internal" href="lib/_distances.html#module-MDAnalysis.lib._distances" title="MDAnalysis.lib._distances"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib._distances</span></tt></a> contains low level access to the
+<p><a class="reference internal" href="lib/_distances.html#module-MDAnalysis.lib._distances" title="MDAnalysis.lib._distances"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib._distances</span></code></a> contains low level access to the
 MDAnalysis&#8217; Cython functions in <cite>distances</cite>.  These have little to no
 error checking done on inputs so should be used with
-caution. <a class="reference internal" href="lib/parallel.html#module-MDAnalysis.lib.parallel" title="MDAnalysis.lib.parallel"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.parallel</span></tt></a> contains parallelized
+caution. <a class="reference internal" href="lib/parallel.html#module-MDAnalysis.lib.parallel" title="MDAnalysis.lib.parallel"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.parallel</span></code></a> contains parallelized
 implementations for some these algorithms.</p>
-<p><a class="reference internal" href="lib/transformations.html#module-MDAnalysis.lib.transformations" title="MDAnalysis.lib.transformations"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.transformations</span></tt></a> contains a multitude of
+<p><a class="reference internal" href="lib/transformations.html#module-MDAnalysis.lib.transformations" title="MDAnalysis.lib.transformations"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.transformations</span></code></a> contains a multitude of
 matrix operations for manipulating coordinate data.</p>
-<p><a class="reference internal" href="lib/qcprot.html#module-MDAnalysis.lib.qcprot" title="MDAnalysis.lib.qcprot"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></tt></a> contains a fast implementation of
+<p><a class="reference internal" href="lib/qcprot.html#module-MDAnalysis.lib.qcprot" title="MDAnalysis.lib.qcprot"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></code></a> contains a fast implementation of
 superposition by minimizing the RMSD.</p>
-<p><a class="reference internal" href="lib/util.html#module-MDAnalysis.lib.util" title="MDAnalysis.lib.util"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.util</span></tt></a> contains various file, string
+<p><a class="reference internal" href="lib/util.html#module-MDAnalysis.lib.util" title="MDAnalysis.lib.util"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.util</span></code></a> contains various file, string
 and mathematical utility functions.</p>
+<dl class="docutils">
+<dt><a class="reference internal" href="lib/NeighborSearch.html#module-MDAnalysis.lib.NeighborSearch" title="MDAnalysis.lib.NeighborSearch"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.lib.NeighborSearch</span></code></a> contains classes to do neighbor searches</dt>
+<dd>with MDAnalysis objects.</dd>
+</dl>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="lib/distances.html">9.1. Fast distance array computation &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.distances</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="lib/_distances.html">9.2. Distance calculation library &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib._distances</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="lib/KDTree_modules.html">9.3. KDTree module</a></li>
-<li class="toctree-l1"><a class="reference internal" href="lib/log.html">9.4. Setting up logging &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.log</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="lib/mdamath.html">9.5. Mathematical helper functions &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.mdamath</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lib/distances.html">9.1. Fast distance array computation &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.distances</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lib/_distances.html">9.2. Distance calculation library &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib._distances</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lib/NeighborSearch.html">9.3. Neighbor Search wrapper for MDAnalysis &#8212; :mod: <cite>MDAnalysis.lib.NeighborSearch</cite></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lib/log.html">9.4. Setting up logging &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.log</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lib/mdamath.html">9.5. Mathematical helper functions &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.mdamath</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="lib/parallel.html">9.6. Parallel algorithms for MDAnalysis</a></li>
-<li class="toctree-l1"><a class="reference internal" href="lib/transformations.html">9.7. Homogeneous Transformation Matrices and Quaternions &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.transformations</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="lib/qcprot.html">9.8. Fast QCP RMSD structure alignment &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="lib/util.html">9.9. Helper functions &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.util</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lib/transformations.html">9.7. Homogeneous Transformation Matrices and Quaternions &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.transformations</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lib/qcprot.html">9.8. Fast QCP RMSD structure alignment &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.qcprot</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lib/util.html">9.9. Helper functions &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.util</span></code></a></li>
 </ul>
 </div>
 </div>
@@ -126,7 +130,7 @@ <h3>Quick search</h3>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -141,10 +145,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="visualization/streamlines_3D.html" title="8.1.2. 3D Streamplot"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -154,7 +158,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/overview.html b/package/doc/html/documentation_pages/overview.html
index 3767e890d00..05c818a8f64 100644
--- a/package/doc/html/documentation_pages/overview.html
+++ b/package/doc/html/documentation_pages/overview.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>1. Overview over MDAnalysis &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>1. Overview over MDAnalysis &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="2. Selection Commands" href="selections.html" />
     <link rel="prev" title="MDAnalysis documentation" href="../index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -50,10 +48,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../index.html" title="MDAnalysis documentation"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
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               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -77,12 +75,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="selections.html"
                         title="next chapter">2. Selection Commands</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/overview.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/overview.txt"
+            rel="nofollow">Show Source</a></li>
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+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -101,7 +101,7 @@ <h3>Quick search</h3>
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-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="overview-over-mdanalysis">
 <h1>1. Overview over MDAnalysis<a class="headerlink" href="#overview-over-mdanalysis" title="Permalink to this headline">¶</a></h1>
@@ -111,15 +111,15 @@ <h1>1. Overview over MDAnalysis<a class="headerlink" href="#overview-over-mdanal
 objects. Each object has a number of operations defined on itself
 (also known as &#8220;methods&#8221;) and also contains values describing the
 object (&#8220;attributes&#8221;). For example, a
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> object has a
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass" title="MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass"><tt class="xref py py-meth docutils literal"><span class="pre">centerOfMass()</span></tt></a> method that
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> object has a
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.center_of_mass" title="MDAnalysis.core.AtomGroup.AtomGroup.center_of_mass"><code class="xref py py-meth docutils literal"><span class="pre">center_of_mass()</span></code></a> method that
 returns the center of mass of the group of atoms. It also contains an
-attribute called <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="MDAnalysis.core.AtomGroup.AtomGroup.residues"><tt class="xref py py-attr docutils literal"><span class="pre">residues</span></tt></a>
+attribute called <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.residues" title="MDAnalysis.core.AtomGroup.AtomGroup.residues"><code class="xref py py-attr docutils literal"><span class="pre">residues</span></code></a>
 that lists all the residues that belong to the group. Using methods
-such as <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a>
-(which uses <a class="reference external" href="http://www.charmm.org/documentation/c37b1/select.html">CHARMM-style</a> atom <a class="reference internal" href="selections.html#selection-commands-label"><em>Selection Commands</em></a>) one
+such as <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.select_atoms" title="MDAnalysis.core.AtomGroup.AtomGroup.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a>
+(which uses <a class="reference external" href="http://www.charmm.org/documentation/c37b1/select.html">CHARMM-style</a> atom <a class="reference internal" href="selections.html#selection-commands-label"><span>Selection Commands</span></a>) one
 can create new objects (in this case, another
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>).</p>
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>).</p>
 <p>A typical usage pattern is to iterate through a trajectory and analyze
 coordinates for every frame. In the following example the end-to-end distance
 of a protein and the radius of gyration of the backbone atoms are calculated:</p>
@@ -133,7 +133,7 @@ <h1>1. Overview over MDAnalysis<a class="headerlink" href="#overview-over-mdanal
 <span class="k">for</span> <span class="n">ts</span> <span class="ow">in</span> <span class="n">u</span><span class="o">.</span><span class="n">trajectory</span><span class="p">:</span>     <span class="c"># iterate through all frames</span>
   <span class="n">r</span> <span class="o">=</span> <span class="n">cterm</span><span class="o">.</span><span class="n">pos</span> <span class="o">-</span> <span class="n">nterm</span><span class="o">.</span><span class="n">pos</span> <span class="c"># end-to-end vector from atom positions</span>
   <span class="n">d</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">norm</span><span class="p">(</span><span class="n">r</span><span class="p">)</span>  <span class="c"># end-to-end distance</span>
-  <span class="n">rgyr</span> <span class="o">=</span> <span class="n">bb</span><span class="o">.</span><span class="n">radiusOfGyration</span><span class="p">()</span>  <span class="c"># method of a AtomGroup; updates with each frame</span>
+  <span class="n">rgyr</span> <span class="o">=</span> <span class="n">bb</span><span class="o">.</span><span class="n">radius_of_gyration</span><span class="p">()</span>  <span class="c"># method of a AtomGroup; updates with each frame</span>
   <span class="k">print</span> <span class="s">&quot;frame = </span><span class="si">%d</span><span class="s">: d = </span><span class="si">%f</span><span class="s"> Angstroem, Rgyr = </span><span class="si">%f</span><span class="s"> Angstroem&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">ts</span><span class="o">.</span><span class="n">frame</span><span class="p">,</span> <span class="n">d</span><span class="p">,</span> <span class="n">rgyr</span><span class="p">)</span>
 </pre></div>
 </div>
@@ -149,7 +149,7 @@ <h2>1.1. Using MDAnalysis in python<a class="headerlink" href="#using-mdanalysis
 </pre></div>
 </div>
 <p>The idea behind MDAnalysis is to get trajectory data into <a class="reference external" href="http://numpy.scipy.org">NumPy</a>
-<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> arrays, where it can then be easily manipulated using
+<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><code class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></code></a> arrays, where it can then be easily manipulated using
 all the power in <a class="reference external" href="http://numpy.scipy.org">NumPy</a> and <a class="reference external" href="http://www.scipy.org/">SciPy</a>.</p>
 <p>MDAnalysis works well both in scripts and in interactive use. The developers
 very much recommend using MDAnalysis from within the <a class="reference external" href="http://ipython.scipy.org/">IPython</a> Python shell.  It
@@ -157,8 +157,8 @@ <h2>1.1. Using MDAnalysis in python<a class="headerlink" href="#using-mdanalysis
 online help), do analysis and immediately plot results. The examples in this manual
 are typically run from an interactive <strong class="program">ipython</strong> session.</p>
 <p>Invariably, a MDAnalysis session starts with loading data into the
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> class (which can be accessed
-as <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt>):</p>
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> class (which can be accessed
+as <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code>):</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">MDAnalysis</span> <span class="kn">import</span> <span class="o">*</span>
 <span class="n">universe</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">topology</span><span class="p">,</span> <span class="n">trajectory</span><span class="p">)</span>
 </pre></div>
@@ -182,39 +182,39 @@ <h2>1.1. Using MDAnalysis in python<a class="headerlink" href="#using-mdanalysis
 <span class="gp">&gt;&gt;&gt; </span><span class="n">u</span> <span class="o">=</span> <span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span> <span class="n">DCD</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>(The <tt class="docutils literal"><span class="pre">&gt;&gt;&gt;</span></tt> signs are the Python input prompt and are not to be typed; they
+<p>(The <code class="docutils literal"><span class="pre">&gt;&gt;&gt;</span></code> signs are the Python input prompt and are not to be typed; they
 just make clear in the examples what is input and what is output.)</p>
-<p>The <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> contains a number of important attributes,
+<p>The <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> contains a number of important attributes,
 the most important ones of which is
-<tt class="xref py py-attr docutils literal"><span class="pre">atoms</span></tt>:</p>
+<code class="xref py py-attr docutils literal"><span class="pre">atoms</span></code>:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="k">print</span> <span class="n">u</span><span class="o">.</span><span class="n">atoms</span>
 <span class="go">&lt;AtomGroup with 3341 atoms&gt;</span>
 </pre></div>
 </div>
-<p><tt class="xref py py-attr docutils literal"><span class="pre">Universe.atoms</span></tt> is a
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> and can be thought of as
-list consisting of <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a>
-objects. The <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> is the
+<p><code class="xref py py-attr docutils literal"><span class="pre">Universe.atoms</span></code> is a
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> and can be thought of as
+list consisting of <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a>
+objects. The <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> is the
 elementary and fundamental object in MDAnalysis.</p>
-<p>The <tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.Universe.trajectory</span></tt> attribute gives access to the coordinates
+<p>The <code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.Universe.trajectory</span></code> attribute gives access to the coordinates
 over time:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="k">print</span> <span class="n">u</span><span class="o">.</span><span class="n">trajectory</span>
 <span class="go">&lt; DCDReader &#39;/..../MDAnalysis/tests/data/adk_dims.dcd&#39; with 98 frames of 3341 atoms (0 fixed) &gt;</span>
 </pre></div>
 </div>
-<p>Finally, the <tt class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.Universe.select_atoms()</span></tt> method generates a new
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> according to a selection criterion</p>
+<p>Finally, the <code class="xref py py-meth docutils literal"><span class="pre">MDAnalysis.Universe.select_atoms()</span></code> method generates a new
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> according to a selection criterion</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">calphas</span> <span class="o">=</span> <span class="n">u</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;name CA&quot;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="k">print</span> <span class="n">calphas</span>
 <span class="go">&lt;AtomGroup with 214 atoms&gt;</span>
 </pre></div>
 </div>
-<p>as described in <a class="reference internal" href="selections.html#selection-commands-label"><em>Selection Commands</em></a>.</p>
+<p>as described in <a class="reference internal" href="selections.html#selection-commands-label"><span>Selection Commands</span></a>.</p>
 </div>
 <div class="section" id="examples">
 <h2>1.2. Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
 <p>The easiest way to get started with MDAnalysis is to read this
-introduction and the chapter on <a class="reference internal" href="selections.html#selection-commands-label"><em>Selection Commands</em></a> and then
+introduction and the chapter on <a class="reference internal" href="selections.html#selection-commands-label"><span>Selection Commands</span></a> and then
 explore the package interactively in <a class="reference external" href="http://ipython.scipy.org/">IPython</a> or another interactive
 Python interpreter.</p>
 <div class="section" id="included-trajectories">
@@ -229,7 +229,7 @@ <h3>1.2.1. Included trajectories<a class="headerlink" href="#included-trajectori
 </pre></div>
 </div>
 <p>The PSF and DCD file are a closed-form-to-open-form transition of
-Adenylate Kinase (from <a class="reference internal" href="#beckstein2009">[Beckstein2009]</a>) and the PDB+XTC file are ten
+Adenylate Kinase (from <a class="reference internal" href="#beckstein2009" id="id1">[Beckstein2009]</a>) and the PDB+XTC file are ten
 frames from a Gromacs simulation of AdK solvated in TIP4P water with
 the OPLS/AA force field.</p>
 <table class="docutils citation" frame="void" id="beckstein2009" rules="none">
@@ -251,13 +251,13 @@ <h3>1.2.2. Code snippets<a class="headerlink" href="#code-snippets" title="Perma
 <p>For instance, there is code that shows how to</p>
 <ul class="simple">
 <li>fit a trajectory to a reference structure using the QCP
-RMSD-alignment code in <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.qcprot</span></tt>
+RMSD-alignment code in <code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.core.qcprot</span></code>
 (<a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/rmsfit_qcp.py">rmsfit_qcp.py</a>);</li>
 <li>do a block-averaging error analysis (<a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/blocks.py">blocks.py</a>);</li>
 <li>calculate a potential profile across a membrane (<a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/potential_profile.py">potential_profile.py</a>);</li>
-<li>do a native contact analysis using <a class="reference internal" href="analysis/contacts.html#module-MDAnalysis.analysis.contacts" title="MDAnalysis.analysis.contacts"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></tt></a> (<a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/nativecontacts.py">nativecontacts.py</a>)</li>
+<li>do a native contact analysis using <a class="reference internal" href="analysis/contacts.html#module-MDAnalysis.analysis.contacts" title="MDAnalysis.analysis.contacts"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></code></a> (<a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/nativecontacts.py">nativecontacts.py</a>)</li>
 <li>get the lipid composition of the individual leaflets of a bilayer
-using <a class="reference internal" href="analysis/leaflet.html#module-MDAnalysis.analysis.leaflet" title="MDAnalysis.analysis.leaflet"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.leaflet</span></tt></a> (<a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/membrane-leaflets.py">membrane-leaflets.py</a>);</li>
+using <a class="reference internal" href="analysis/leaflet.html#module-MDAnalysis.analysis.leaflet" title="MDAnalysis.analysis.leaflet"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.leaflet</span></code></a> (<a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/membrane-leaflets.py">membrane-leaflets.py</a>);</li>
 <li>define the multimeric states of a number of transmembrane peptides
 via clustering (<a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/multimers-analysis.py">multimers-analysis.py</a>);</li>
 <li>convert between trajectory formats (e.g. <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/dcd2xtc.py">dcd2xtc.py</a> or <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/amber2dcd.py">amber2dcd.py</a>)</li>
@@ -274,7 +274,7 @@ <h3>1.2.2. Code snippets<a class="headerlink" href="#code-snippets" title="Perma
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -289,10 +289,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../index.html" title="MDAnalysis documentation"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -302,7 +302,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/references.html b/package/doc/html/documentation_pages/references.html
index 639dbbb9fdd..a6d0b687d15 100644
--- a/package/doc/html/documentation_pages/references.html
+++ b/package/doc/html/documentation_pages/references.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>13. References &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>13. References &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="prev" title="12. Custom exceptions and warnings — MDAnalysis.exceptions" href="exceptions.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -46,10 +44,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="exceptions.html" title="12. Custom exceptions and warnings — MDAnalysis.exceptions"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../index.html">
               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -65,13 +63,15 @@ <h3><a href="../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="exceptions.html"
-                        title="previous chapter">12. Custom exceptions and warnings &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.exceptions</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/references.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="previous chapter">12. Custom exceptions and warnings &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.exceptions</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/references.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -90,7 +90,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="references">
 <span id="id1"></span><h1>13. References<a class="headerlink" href="#references" title="Permalink to this headline">¶</a></h1>
@@ -106,9 +106,9 @@ <h2>13.1. Citation for the whole MDAnalysis library<a class="headerlink" href="#
 </div>
 <div class="section" id="citations-for-included-algorithms-and-modules">
 <span id="references-components"></span><h2>13.2. Citations for included algorithms and modules<a class="headerlink" href="#citations-for-included-algorithms-and-modules" title="Permalink to this headline">¶</a></h2>
-<p>If you use the RMSD calculation (<a class="reference internal" href="analysis/rms.html#module-MDAnalysis.analysis.rms" title="MDAnalysis.analysis.rms"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></tt></a>) or
-alignment code (<a class="reference internal" href="analysis/align.html#module-MDAnalysis.analysis.align" title="MDAnalysis.analysis.align"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.align</span></tt></a>) that uses the
-<tt class="xref py py-mod docutils literal"><span class="pre">qcprot</span></tt> module please also cite</p>
+<p>If you use the RMSD calculation (<a class="reference internal" href="analysis/rms.html#module-MDAnalysis.analysis.rms" title="MDAnalysis.analysis.rms"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.rms</span></code></a>) or
+alignment code (<a class="reference internal" href="analysis/align.html#module-MDAnalysis.analysis.align" title="MDAnalysis.analysis.align"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.align</span></code></a>) that uses the
+<code class="xref py py-mod docutils literal"><span class="pre">qcprot</span></code> module please also cite</p>
 <ul class="simple">
 <li>Douglas L. Theobald. Rapid calculation of RMSD using a
 quaternion-based characteristic polynomial. <em>Acta
@@ -118,21 +118,21 @@ <h2>13.1. Citation for the whole MDAnalysis library<a class="headerlink" href="#
 superpositions. <em>J. Comput. Chem.</em> <strong>31</strong> (2010), 1561–1563.</li>
 </ul>
 <p>If you use the helix analysis algorithm <a class="reference external" href="http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html">HELANAL</a> in
-<a class="reference internal" href="analysis/helanal.html#module-MDAnalysis.analysis.helanal" title="MDAnalysis.analysis.helanal"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.helanal</span></tt></a> please cite</p>
+<a class="reference internal" href="analysis/helanal.html#module-MDAnalysis.analysis.helanal" title="MDAnalysis.analysis.helanal"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.helanal</span></code></a> please cite</p>
 <ul class="simple">
 <li>Bansal M, Kumar S, Velavan R. HELANAL — A program to characterise
 helix geometry in proteins. <em>J. Biomol. Struct. Dyn.</em> <strong>17</strong>
 (2000), 811–819</li>
 </ul>
 <p>If you use the GNM trajectory analysis code in
-<a class="reference internal" href="analysis/gnm.html#module-MDAnalysis.analysis.gnm" title="MDAnalysis.analysis.gnm"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.gnm</span></tt></a> please cite</p>
+<a class="reference internal" href="analysis/gnm.html#module-MDAnalysis.analysis.gnm" title="MDAnalysis.analysis.gnm"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.gnm</span></code></a> please cite</p>
 <ul class="simple">
 <li>Benjamin A. Hall, Samantha L. Kaye, Andy Pang, Rafael Perera, and
 Philip C. Biggin. Characterization of Protein Conformational
 States by Normal-Mode Frequencies. <em>JACS</em> <strong>129</strong> (2007), 11394–11401.</li>
 </ul>
 <p>If you use the water analysis code in
-<a class="reference internal" href="analysis/waterdynamics.html#module-MDAnalysis.analysis.waterdynamics" title="MDAnalysis.analysis.waterdynamics"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></tt></a> please cite</p>
+<a class="reference internal" href="analysis/waterdynamics.html#module-MDAnalysis.analysis.waterdynamics" title="MDAnalysis.analysis.waterdynamics"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></code></a> please cite</p>
 <ul class="simple">
 <li>Araya-Secchi, R., Tomas Perez-Acle, Seung-gu Kang, Tien Huynh,
 Alejandro Bernardin, Yerko Escalona, Jose-Antonio Garate, Agustin
@@ -151,7 +151,7 @@ <h2>13.1. Citation for the whole MDAnalysis library<a class="headerlink" href="#
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -163,10 +163,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="exceptions.html" title="12. Custom exceptions and warnings — MDAnalysis.exceptions"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -176,7 +176,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections.html b/package/doc/html/documentation_pages/selections.html
index 180e4aaedf2..4b301d44edb 100644
--- a/package/doc/html/documentation_pages/selections.html
+++ b/package/doc/html/documentation_pages/selections.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>2. Selection Commands &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>2. Selection Commands &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="3. Analysis modules" href="analysis_modules.html" />
     <link rel="prev" title="1. Overview over MDAnalysis" href="overview.html" /> 
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
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       <ul>
         <li class="right" style="margin-right: 10px">
@@ -50,10 +48,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="overview.html" title="1. Overview over MDAnalysis"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../index.html">
               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -88,12 +86,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="analysis_modules.html"
                         title="next chapter">3. Analysis modules</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/selections.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/selections.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -112,20 +112,20 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="selection-commands">
 <span id="selection-commands-label"></span><h1>2. Selection Commands<a class="headerlink" href="#selection-commands" title="Permalink to this headline">¶</a></h1>
-<p>Once you have the <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-meth docutils literal"><span class="pre">Universe()</span></tt></a> object, you can
+<p>Once you have the <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-meth docutils literal"><span class="pre">Universe()</span></code></a> object, you can
 select atoms (using a syntax very similar to <a class="reference external" href="http://www.charmm.org/documentation/c37b1/select.html">CHARMM&#8217;s atom selection
 syntax</a>):</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">kalp</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;segid KALP&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>The <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt></a> of a
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a> returns a
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a>, so you can use all the methods
-defined for AtomGroups on them. Selections always return an <tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt> with
+<p>The <a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.select_atoms" title="MDAnalysis.core.AtomGroup.Universe.select_atoms"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code></a> of a
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a> returns a
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a>, so you can use all the methods
+defined for AtomGroups on them. Selections always return an <code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code> with
 atoms sorted according to their index in the topology (this is to ensure that
 there aren&#8217;t any duplicates, which can happen with complicated selections).</p>
 <p>One can group subselections using parentheses:</p>
@@ -135,7 +135,7 @@ <h3>Quick search</h3>
 </div>
 <p>Almost all the basic CHARMM selections work.</p>
 <p>It is also possible to export selections for external software
-packages with the help of <a class="reference internal" href="selections_modules.html#selection-exporters"><em>Selection exporters</em></a>.</p>
+packages with the help of <a class="reference internal" href="selections_modules.html#selection-exporters"><span>Selection exporters</span></a>.</p>
 <div class="section" id="selection-keywords">
 <h2>2.1. Selection Keywords<a class="headerlink" href="#selection-keywords" title="Permalink to this headline">¶</a></h2>
 <p>The following describes all selection keywords currently understood by the
@@ -143,12 +143,12 @@ <h2>2.1. Selection Keywords<a class="headerlink" href="#selection-keywords" titl
 <ul class="simple">
 <li>Keywords are case sensitive.</li>
 <li>Atoms are automatically sequentially ordered in a resulting selection
-(see notes below on <a class="reference internal" href="#ordered-selections-label"><em>Ordered selections</em></a> for how to circumvent this if
+(see notes below on <a class="reference internal" href="#ordered-selections-label"><span>Ordered selections</span></a> for how to circumvent this if
 necessary).</li>
 <li>Selections are parsed left to right and parentheses can be used for
 grouping.</li>
 <li>Currently, only &#8220;stemming&#8221; is implemented as a primitive form of pattern
-matching: Using the <tt class="docutils literal"><span class="pre">*</span></tt> character in a string such as <tt class="docutils literal"><span class="pre">GL*</span></tt> selects
+matching: Using the <code class="docutils literal"><span class="pre">*</span></code> character in a string such as <code class="docutils literal"><span class="pre">GL*</span></code> selects
 all strings that start with &#8220;GL&#8221; such as &#8220;GLU&#8221;, &#8220;GLY&#8221;, &#8220;GLX29&#8221;, &#8220;GLN&#8221;.</li>
 </ul>
 <div class="section" id="simple-selections">
@@ -160,20 +160,20 @@ <h3>2.1.1. Simple selections<a class="headerlink" href="#simple-selections" titl
 is identfied by a hard-coded set of residue names so it  may not
 work for esoteric residues.</dd>
 <dt>segid <em>seg-name</em></dt>
-<dd>select by segid (as given in the topology), e.g. <tt class="docutils literal"><span class="pre">segid</span> <span class="pre">4AKE</span></tt> or <tt class="docutils literal"><span class="pre">segid</span> <span class="pre">DMPC</span></tt></dd>
+<dd>select by segid (as given in the topology), e.g. <code class="docutils literal"><span class="pre">segid</span> <span class="pre">4AKE</span></code> or <code class="docutils literal"><span class="pre">segid</span> <span class="pre">DMPC</span></code></dd>
 <dt>resid <em>residue-number-range</em></dt>
 <dd>resid can take a single residue number or a range of numbers. A range
 consists of two numbers separated by a colon (inclusive) such
-as <tt class="docutils literal"><span class="pre">resid</span> <span class="pre">1:5</span></tt>. A residue number (&#8220;resid&#8221;) is taken directly from the
+as <code class="docutils literal"><span class="pre">resid</span> <span class="pre">1:5</span></code>. A residue number (&#8220;resid&#8221;) is taken directly from the
 topology.</dd>
 <dt>resnum <em>resnum-number-range</em></dt>
 <dd>resnum is the canonical residue number; typically it is set to the residue id
 in the original PDB structure.</dd>
 <dt>resname <em>residue-name</em></dt>
-<dd>select by residue name, e.g. <tt class="docutils literal"><span class="pre">resname</span> <span class="pre">LYS</span></tt></dd>
+<dd>select by residue name, e.g. <code class="docutils literal"><span class="pre">resname</span> <span class="pre">LYS</span></code></dd>
 <dt>name <em>atom-name</em></dt>
 <dd>select by atom name (as given in the topology). Often, this is force
-field dependent. Example: <tt class="docutils literal"><span class="pre">name</span> <span class="pre">CA</span></tt> (for C&amp;alpha; atoms) or <tt class="docutils literal"><span class="pre">name</span> <span class="pre">OW</span></tt> (for SPC water oxygen)</dd>
+field dependent. Example: <code class="docutils literal"><span class="pre">name</span> <span class="pre">CA</span></code> (for C&amp;alpha; atoms) or <code class="docutils literal"><span class="pre">name</span> <span class="pre">OW</span></code> (for SPC water oxygen)</dd>
 <dt>type <em>atom-type</em></dt>
 <dd>select by atom type; this is either a string or a number and depends on
 the force field; it is read from the topology file (e.g. the CHARMM PSF
@@ -181,7 +181,7 @@ <h3>2.1.1. Simple selections<a class="headerlink" href="#simple-selections" titl
 PDB or GRO file is used as a topology.</dd>
 <dt>atom <em>seg-name</em>  <em>residue-number</em>  <em>atom-name</em></dt>
 <dd>a selector for a single atom consisting of segid resid atomname,
-e.g. <tt class="docutils literal"><span class="pre">DMPC</span> <span class="pre">1</span> <span class="pre">C2</span></tt> selects the C2 carbon of the first residue of the DMPC
+e.g. <code class="docutils literal"><span class="pre">DMPC</span> <span class="pre">1</span> <span class="pre">C2</span></code> selects the C2 carbon of the first residue of the DMPC
 segment</dd>
 </dl>
 </div></blockquote>
@@ -191,10 +191,10 @@ <h3>2.1.2. Boolean<a class="headerlink" href="#boolean" title="Permalink to this
 <blockquote>
 <div><dl class="docutils">
 <dt>not</dt>
-<dd>all atoms not in the selection, e.g. <tt class="docutils literal"><span class="pre">not</span> <span class="pre">protein</span></tt> selects all atoms that aren&#8217;t part of a protein</dd>
+<dd>all atoms not in the selection, e.g. <code class="docutils literal"><span class="pre">not</span> <span class="pre">protein</span></code> selects all atoms that aren&#8217;t part of a protein</dd>
 <dt>and, or</dt>
 <dd>combine two selections according to the rules of boolean algebra,
-e.g. <tt class="docutils literal"><span class="pre">protein</span> <span class="pre">and</span> <span class="pre">not</span> <span class="pre">(resname</span> <span class="pre">ALA</span> <span class="pre">or</span> <span class="pre">resname</span> <span class="pre">LYS)</span></tt> selects all atoms
+e.g. <code class="docutils literal"><span class="pre">protein</span> <span class="pre">and</span> <span class="pre">not</span> <span class="pre">(resname</span> <span class="pre">ALA</span> <span class="pre">or</span> <span class="pre">resname</span> <span class="pre">LYS)</span></code> selects all atoms
 that belong to a protein, but are not in a lysine or alanine residue</dd>
 </dl>
 </div></blockquote>
@@ -205,42 +205,43 @@ <h3>2.1.3. Geometric<a class="headerlink" href="#geometric" title="Permalink to
 <div><dl class="docutils">
 <dt>around <em>distance</em>  <em>selection</em></dt>
 <dd>selects all atoms a certain cutoff away from another selection,
-e.g. <tt class="docutils literal"><span class="pre">around</span> <span class="pre">3.5</span> <span class="pre">protein</span></tt> selects all atoms not belonging to protein
+e.g. <code class="docutils literal"><span class="pre">around</span> <span class="pre">3.5</span> <span class="pre">protein</span></code> selects all atoms not belonging to protein
 that are within 3.5 Angstroms from the protein</dd>
 <dt>sphlayer <em>innerRadius</em> <em>externalRadius</em> <em>selection</em></dt>
 <dd>selects all atoms within a spherical layer centered in the center of geometry (COG) of a given selection,
-e.g. <tt class="docutils literal"><span class="pre">sphlayer</span> <span class="pre">2.4</span> <span class="pre">6.0</span> <span class="pre">(</span> <span class="pre">protein</span> <span class="pre">and</span> <span class="pre">(</span> <span class="pre">resid</span> <span class="pre">130</span> <span class="pre">or</span> <span class="pre">resid</span> <span class="pre">80</span> <span class="pre">)</span> <span class="pre">)</span></tt> selects the center of geometry of protein, resid 130, resid 80
+e.g. <code class="docutils literal"><span class="pre">sphlayer</span> <span class="pre">2.4</span> <span class="pre">6.0</span> <span class="pre">(</span> <span class="pre">protein</span> <span class="pre">and</span> <span class="pre">(</span> <span class="pre">resid</span> <span class="pre">130</span> <span class="pre">or</span> <span class="pre">resid</span> <span class="pre">80</span> <span class="pre">)</span> <span class="pre">)</span></code> selects the center of geometry of protein, resid 130, resid 80
 and creates a spherical layer of inner radius 2.4 and external radius 6.0 around the COG.</dd>
 <dt>sphzone <em>externalRadius</em> <em>selection</em></dt>
 <dd>selects all atoms within a spherical zone centered in the center of geometry (COG) of a given selection,
-e.g. <tt class="docutils literal"><span class="pre">sphzone</span> <span class="pre">6.0</span> <span class="pre">(</span> <span class="pre">protein</span> <span class="pre">and</span> <span class="pre">(</span> <span class="pre">resid</span> <span class="pre">130</span> <span class="pre">or</span> <span class="pre">resid</span> <span class="pre">80</span> <span class="pre">)</span> <span class="pre">)</span></tt> selects the center of geometry of protein, resid 130,
+e.g. <code class="docutils literal"><span class="pre">sphzone</span> <span class="pre">6.0</span> <span class="pre">(</span> <span class="pre">protein</span> <span class="pre">and</span> <span class="pre">(</span> <span class="pre">resid</span> <span class="pre">130</span> <span class="pre">or</span> <span class="pre">resid</span> <span class="pre">80</span> <span class="pre">)</span> <span class="pre">)</span></code> selects the center of geometry of protein, resid 130,
 resid 80 and creates a sphere of radius 6.0 around the COG.</dd>
 <dt>cylayer <em>innerRadius</em> <em>externalRadius</em> <em>zMax</em> <em>zMin</em> <em>selection</em></dt>
 <dd>selects all atoms within a cylindric layer centered in the center of geometry (COG) of a given selection,
-e.g. <tt class="docutils literal"><span class="pre">cylayer</span> <span class="pre">5</span> <span class="pre">10</span> <span class="pre">10</span> <span class="pre">-8</span> <span class="pre">protein</span></tt> selects the center of geometry of protein,
+e.g. <code class="docutils literal"><span class="pre">cylayer</span> <span class="pre">5</span> <span class="pre">10</span> <span class="pre">10</span> <span class="pre">-8</span> <span class="pre">protein</span></code> selects the center of geometry of protein,
 and creates a cylindrical layer of inner radius 5, external radius 10 centered on the COG. In z, the cylinder
 extends from 10 above the COG to 8 below. Positive values for <em>zMin</em>, or negative ones for <em>zMax</em>,
 are allowed.</dd>
 <dt>cyzone <em>externalRadius</em> <em>zMax</em> <em>zMin</em> <em>selection</em></dt>
 <dd>selects all atoms within a cylindric zone centered in the center of geometry (COG) of a given selection,
-e.g. <tt class="docutils literal"><span class="pre">cyzone</span> <span class="pre">15</span> <span class="pre">4</span> <span class="pre">-8</span> <span class="pre">protein</span> <span class="pre">and</span> <span class="pre">resid</span> <span class="pre">42</span></tt> selects the center of geometry of protein and resid 42,
+e.g. <code class="docutils literal"><span class="pre">cyzone</span> <span class="pre">15</span> <span class="pre">4</span> <span class="pre">-8</span> <span class="pre">protein</span> <span class="pre">and</span> <span class="pre">resid</span> <span class="pre">42</span></code> selects the center of geometry of protein and resid 42,
 and creates a cylinder of external radius 15 centered on the COG. In z, the cylinder
 extends from 4 above the COG to 8 below. Positive values for <em>zMin</em>, or negative ones for <em>zMax</em>,
 are allowed.</dd>
 </dl>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.10.0: </span>keywords <em>cyzone</em> and <em>cylayer</em> now take <em>zMax</em> and <em>zMin</em> to be relative to the COG of
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.10.0: </span>keywords <em>cyzone</em> and <em>cylayer</em> now take <em>zMax</em> and <em>zMin</em> to be relative to the COG of
 <em>selection</em>, instead of absolute z-values in the box.</p>
+</div>
 <dl class="docutils">
 <dt>point <em>x</em> <em>y</em> <em>z</em>  <em>distance</em></dt>
 <dd>selects all atoms within a cutoff of a point in space, make sure
-coordinate is separated by spaces, e.g. <tt class="docutils literal"><span class="pre">point</span> <span class="pre">5.0</span> <span class="pre">5.0</span> <span class="pre">5.0</span>&nbsp; <span class="pre">3.5</span></tt> selects
+coordinate is separated by spaces, e.g. <code class="docutils literal"><span class="pre">point</span> <span class="pre">5.0</span> <span class="pre">5.0</span> <span class="pre">5.0</span>&nbsp; <span class="pre">3.5</span></code> selects
 all atoms within 3.5 Angstroms of the coordinate (5.0, 5.0, 5.0)</dd>
 <dt>prop [abs] <em>property</em>  <em>operator</em>  <em>value</em></dt>
 <dd>selects atoms based on position, using <em>property</em>  <strong>x</strong>, <strong>y</strong>, or
 <strong>z</strong> coordinate. Supports the <strong>abs</strong> keyword (for absolute value) and
-the following <em>operators</em>: <strong>&lt;, &gt;, &lt;=, &gt;=, ==, !=</strong>. For example, <tt class="docutils literal"><span class="pre">prop</span> <span class="pre">z</span> <span class="pre">&gt;=</span> <span class="pre">5.0</span></tt>
-selects all atoms with z coordinate greater than 5.0; <tt class="docutils literal"><span class="pre">prop</span> <span class="pre">abs</span> <span class="pre">z</span> <span class="pre">&lt;=</span> <span class="pre">5.0</span></tt>
+the following <em>operators</em>: <strong>&lt;, &gt;, &lt;=, &gt;=, ==, !=</strong>. For example, <code class="docutils literal"><span class="pre">prop</span> <span class="pre">z</span> <span class="pre">&gt;=</span> <span class="pre">5.0</span></code>
+selects all atoms with z coordinate greater than 5.0; <code class="docutils literal"><span class="pre">prop</span> <span class="pre">abs</span> <span class="pre">z</span> <span class="pre">&lt;=</span> <span class="pre">5.0</span></code>
 selects all atoms within -5.0 &lt;= z &lt;= 5.0.</dd>
 </dl>
 </div></blockquote>
@@ -249,7 +250,7 @@ <h3>2.1.3. Geometric<a class="headerlink" href="#geometric" title="Permalink to
 previous version). However, it does not take periodicity into
 account. The fast algorithm is the default for <em>around</em>. Periodicity
 is only taken into account with the
-<a class="reference internal" href="analysis/distances.html#MDAnalysis.analysis.distances.distance_array" title="MDAnalysis.analysis.distances.distance_array"><tt class="xref py py-func docutils literal"><span class="pre">distance_array()</span></tt></a> functions via a
+<a class="reference internal" href="analysis/distances.html#MDAnalysis.analysis.distances.distance_array" title="MDAnalysis.analysis.distances.distance_array"><code class="xref py py-func docutils literal"><span class="pre">distance_array()</span></code></a> functions via a
 minimum image convention (and this only works for rectangular
 simulation cells). If periodic boundary conditions should be taken
 into account then change the default behaviour of MDAnalysis by setting
@@ -265,13 +266,13 @@ <h3>2.1.4. Similarity and connectivity<a class="headerlink" href="#similarity-an
 <div><dl class="docutils">
 <dt>same <em>subkeyword</em> as <em>selection</em></dt>
 <dd>selects all atoms that have the same <em>subkeyword</em> value as any atom in
-<em>selection</em>. Allowed <em>subkeyword</em> values are the atom properties: <tt class="docutils literal"><span class="pre">name,</span> <span class="pre">type,</span> <span class="pre">resname,</span> <span class="pre">resid,</span> <span class="pre">segid,</span> <span class="pre">mass,</span> <span class="pre">charge,</span> <span class="pre">radius,</span> <span class="pre">bfactor,</span> <span class="pre">resnum</span></tt>,
-the groups an atom belong to: <tt class="docutils literal"><span class="pre">residue,</span> <span class="pre">segment,</span> <span class="pre">fragment</span></tt>, and the atom
-coordinates <tt class="docutils literal"><span class="pre">x,</span> <span class="pre">y,</span> <span class="pre">z</span></tt>.</dd>
+<em>selection</em>. Allowed <em>subkeyword</em> values are the atom properties: <code class="docutils literal"><span class="pre">name,</span> <span class="pre">type,</span> <span class="pre">resname,</span> <span class="pre">resid,</span> <span class="pre">segid,</span> <span class="pre">mass,</span> <span class="pre">charge,</span> <span class="pre">radius,</span> <span class="pre">bfactor,</span> <span class="pre">resnum</span></code>,
+the groups an atom belong to: <code class="docutils literal"><span class="pre">residue,</span> <span class="pre">segment,</span> <span class="pre">fragment</span></code>, and the atom
+coordinates <code class="docutils literal"><span class="pre">x,</span> <span class="pre">y,</span> <span class="pre">z</span></code>.</dd>
 <dt>byres <em>selection</em></dt>
 <dd>selects all atoms that are in the same segment and residue as
 selection, e.g. specify the subselection after the byres keyword.
-<tt class="docutils literal"><span class="pre">byres</span></tt> is a shortcut to <tt class="docutils literal"><span class="pre">same</span> <span class="pre">residue</span> <span class="pre">as</span></tt></dd>
+<code class="docutils literal"><span class="pre">byres</span></code> is a shortcut to <code class="docutils literal"><span class="pre">same</span> <span class="pre">residue</span> <span class="pre">as</span></code></dd>
 </dl>
 </div></blockquote>
 </div>
@@ -281,9 +282,9 @@ <h3>2.1.5. Index<a class="headerlink" href="#index" title="Permalink to this hea
 <div><dl class="docutils">
 <dt>bynum <em>index-range</em></dt>
 <dd>selects all atoms within a range of (1-based) inclusive indices,
-e.g. <tt class="docutils literal"><span class="pre">bynum</span> <span class="pre">1</span></tt> selects the first atom in the universe; <tt class="docutils literal"><span class="pre">bynum</span> <span class="pre">5:10</span></tt>
+e.g. <code class="docutils literal"><span class="pre">bynum</span> <span class="pre">1</span></code> selects the first atom in the universe; <code class="docutils literal"><span class="pre">bynum</span> <span class="pre">5:10</span></code>
 selects atoms 5 through 10 inclusive. All atoms in the
-<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> are consecutively numbered, and the index
+<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> are consecutively numbered, and the index
 runs from 1 up to the total number of atoms.</dd>
 </dl>
 </div></blockquote>
@@ -293,29 +294,30 @@ <h3>2.1.6. Preexisting selections and modifiers<a class="headerlink" href="#pree
 <blockquote>
 <div><dl class="docutils">
 <dt>group <em>group-name</em></dt>
-<dd>selects the atoms in the <tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt> passed to the function as an
+<dd>selects the atoms in the <code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code> passed to the function as an
 argument named <em>group-name</em>. Only the atoms common to <em>group-name</em> and the
-instance <tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt> was called from will be considered.
+instance <code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code> was called from will be considered.
 <em>group-name</em> will be included in the parsing just by comparison of atom indices.
 This means that it is up to the user to make sure they were defined in an
-appropriate <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt>.</dd>
+appropriate <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code>.</dd>
 <dt>fullgroup <em>group-name</em></dt>
-<dd>just like the <tt class="docutils literal"><span class="pre">group</span></tt> keyword with the difference that all the atoms of
+<dd>just like the <code class="docutils literal"><span class="pre">group</span></code> keyword with the difference that all the atoms of
 <em>group-name</em> are included. The resulting selection may therefore have atoms
-that were initially absent from the instance <tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt> was
+that were initially absent from the instance <code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code> was
 called from.</dd>
 </dl>
-<p class="deprecated">
-<span class="versionmodified">Deprecated since version 0.11: </span>The use of <tt class="docutils literal"><span class="pre">fullgroup</span></tt> has been deprecated in favor of the equivalent <tt class="docutils literal"><span class="pre">global</span> <span class="pre">group</span></tt>.</p>
+<div class="deprecated">
+<p><span class="versionmodified">Deprecated since version 0.11: </span>The use of <code class="docutils literal"><span class="pre">fullgroup</span></code> has been deprecated in favor of the equivalent <code class="docutils literal"><span class="pre">global</span> <span class="pre">group</span></code>.</p>
+</div>
 <dl class="docutils">
 <dt>global <em>selection</em></dt>
-<dd>by default, when issuing <tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt> from an <tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt>
+<dd>by default, when issuing <code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code> from an <code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code>
 selections and subselections are returned intersected with the atoms of that instance.
-Prefixing a selection term with <tt class="docutils literal"><span class="pre">global</span></tt> causes its selection to be returned in its entirety.
-As an exmaple, the <tt class="docutils literal"><span class="pre">global</span></tt> keyword allows for <tt class="docutils literal"><span class="pre">lipids.select_atoms(&quot;around</span> <span class="pre">10</span> <span class="pre">global</span> <span class="pre">protein&quot;)</span></tt> &#8212;
-where <tt class="docutils literal"><span class="pre">lipids</span></tt> is a group that does not contain any proteins. Were <tt class="docutils literal"><span class="pre">global</span></tt> it absent the result
-would be an empty selection since the <tt class="docutils literal"><span class="pre">protein</span></tt> subselection would itself be empty.
-When issuing <tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt> from a <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> <tt class="docutils literal"><span class="pre">global</span></tt> is ignored.</dd>
+Prefixing a selection term with <code class="docutils literal"><span class="pre">global</span></code> causes its selection to be returned in its entirety.
+As an exmaple, the <code class="docutils literal"><span class="pre">global</span></code> keyword allows for <code class="docutils literal"><span class="pre">lipids.select_atoms(&quot;around</span> <span class="pre">10</span> <span class="pre">global</span> <span class="pre">protein&quot;)</span></code> &#8212;
+where <code class="docutils literal"><span class="pre">lipids</span></code> is a group that does not contain any proteins. Were <code class="docutils literal"><span class="pre">global</span></code> it absent the result
+would be an empty selection since the <code class="docutils literal"><span class="pre">protein</span></code> subselection would itself be empty.
+When issuing <code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code> from a <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> <code class="docutils literal"><span class="pre">global</span></code> is ignored.</dd>
 </dl>
 </div></blockquote>
 </div>
@@ -324,22 +326,22 @@ <h3>2.1.6. Preexisting selections and modifiers<a class="headerlink" href="#pree
 <h2>2.2. Instant selectors<a class="headerlink" href="#instant-selectors" title="Permalink to this headline">¶</a></h2>
 <p>For interactive work it becomes rather tedious to type common selection strings
 repeatedly. MDAnalysis automatically generates a number of <em>instant selectors</em>
-as attributes of the <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> and number of other levels
+as attributes of the <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> and number of other levels
 of the structural hierarchy, namely for
-<tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt>,
-<tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt>,
-<tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt>,
-<tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt> and
-<tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt>.</p>
+<code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code>,
+<code class="xref py py-class docutils literal"><span class="pre">Residue</span></code>,
+<code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code>,
+<code class="xref py py-class docutils literal"><span class="pre">Segment</span></code> and
+<code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code>.</p>
 <div class="section" id="segment-selector">
 <h3>2.2.1. Segment selector<a class="headerlink" href="#segment-selector" title="Permalink to this headline">¶</a></h3>
 <ul>
-<li><p class="first"><tt class="docutils literal"><span class="pre">universe.&lt;segid&gt;</span></tt> or <tt class="docutils literal"><span class="pre">universe.s&lt;segid&gt;</span></tt> (if <em>&lt;segid&gt;</em> starts with a
+<li><p class="first"><code class="docutils literal"><span class="pre">universe.&lt;segid&gt;</span></code> or <code class="docutils literal"><span class="pre">universe.s&lt;segid&gt;</span></code> (if <em>&lt;segid&gt;</em> starts with a
 number)</p>
 </li>
-<li><p class="first">returns a <tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></p>
+<li><p class="first">returns a <code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></p>
 </li>
-<li><p class="first">works for <tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt> and <tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></p>
+<li><p class="first">works for <code class="xref py py-class docutils literal"><span class="pre">Universe</span></code> and <code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code></p>
 </li>
 <li><dl class="first docutils">
 <dt>example</dt>
@@ -355,11 +357,11 @@ <h3>2.2.1. Segment selector<a class="headerlink" href="#segment-selector" title=
 <div class="section" id="resid-selector">
 <h3>2.2.2. Resid selector<a class="headerlink" href="#resid-selector" title="Permalink to this headline">¶</a></h3>
 <ul>
-<li><p class="first"><tt class="docutils literal"><span class="pre">seg.r&lt;N&gt;</span></tt> selects residue with number <tt class="docutils literal"><span class="pre">&lt;N&gt;</span></tt></p>
+<li><p class="first"><code class="docutils literal"><span class="pre">seg.r&lt;N&gt;</span></code> selects residue with number <code class="docutils literal"><span class="pre">&lt;N&gt;</span></code></p>
 </li>
-<li><p class="first">returns a <tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></p>
+<li><p class="first">returns a <code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></p>
 </li>
-<li><p class="first">works for <tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt> and <tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></p>
+<li><p class="first">works for <code class="xref py py-class docutils literal"><span class="pre">Segment</span></code> and <code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code></p>
 </li>
 <li><dl class="first docutils">
 <dt>example</dt>
@@ -375,11 +377,11 @@ <h3>2.2.2. Resid selector<a class="headerlink" href="#resid-selector" title="Per
 <div class="section" id="residue-name-selector">
 <h3>2.2.3. Residue name selector<a class="headerlink" href="#residue-name-selector" title="Permalink to this headline">¶</a></h3>
 <ul>
-<li><p class="first"><tt class="docutils literal"><span class="pre">seg.&lt;resname&gt;</span></tt> selects residues with residue name <tt class="docutils literal"><span class="pre">&lt;resname&gt;</span></tt></p>
+<li><p class="first"><code class="docutils literal"><span class="pre">seg.&lt;resname&gt;</span></code> selects residues with residue name <code class="docutils literal"><span class="pre">&lt;resname&gt;</span></code></p>
 </li>
-<li><p class="first">returns a <tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt></p>
+<li><p class="first">returns a <code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code></p>
 </li>
-<li><p class="first">works for <tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt> and <tt class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></tt></p>
+<li><p class="first">works for <code class="xref py py-class docutils literal"><span class="pre">Segment</span></code> and <code class="xref py py-class docutils literal"><span class="pre">SegmentGroup</span></code></p>
 </li>
 <li><dl class="first docutils">
 <dt>examples</dt>
@@ -394,29 +396,29 @@ <h3>2.2.3. Residue name selector<a class="headerlink" href="#residue-name-select
 </dd>
 </dl>
 </li>
-<li><p class="first">The result is always a <tt class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></tt>; if no
-residues can be found then a <tt class="xref py py-exc docutils literal"><span class="pre">MDAnalysis.NoDataError</span></tt> is raised.</p>
+<li><p class="first">The result is always a <code class="xref py py-class docutils literal"><span class="pre">ResidueGroup</span></code>; if no
+residues can be found then a <code class="xref py py-exc docutils literal"><span class="pre">MDAnalysis.NoDataError</span></code> is raised.</p>
 </li>
 </ul>
 </div>
 <div class="section" id="atom-name-selector">
 <h3>2.2.4. Atom name selector<a class="headerlink" href="#atom-name-selector" title="Permalink to this headline">¶</a></h3>
 <ul>
-<li><p class="first"><tt class="docutils literal"><span class="pre">g.&lt;atomname&gt;</span></tt> selects a single atom or a group of atoms with name
-<tt class="docutils literal"><span class="pre">&lt;atomname&gt;</span></tt></p>
+<li><p class="first"><code class="docutils literal"><span class="pre">g.&lt;atomname&gt;</span></code> selects a single atom or a group of atoms with name
+<code class="docutils literal"><span class="pre">&lt;atomname&gt;</span></code></p>
 </li>
 <li><dl class="first docutils">
 <dt>returns</dt>
 <dd><ul class="first last simple">
-<li>a <tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt> if only a single atom was found,</li>
-<li>a <tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt> if more than one atom was
+<li>a <code class="xref py py-class docutils literal"><span class="pre">Atom</span></code> if only a single atom was found,</li>
+<li>a <code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code> if more than one atom was
 found, or</li>
-<li>raises a <tt class="xref py py-exc docutils literal"><span class="pre">MDAnalysis.SelectionError</span></tt> if no atom was found.</li>
+<li>raises a <code class="xref py py-exc docutils literal"><span class="pre">MDAnalysis.SelectionError</span></code> if no atom was found.</li>
 </ul>
 </dd>
 </dl>
 </li>
-<li><p class="first">works for any group derived from <tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt>
+<li><p class="first">works for any group derived from <code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code>
 (i.e. all the ones mentioned above)</p>
 </li>
 <li><dl class="first docutils">
@@ -439,8 +441,8 @@ <h3>2.2.4. Atom name selector<a class="headerlink" href="#atom-name-selector" ti
 </div>
 <div class="section" id="ordered-selections">
 <span id="ordered-selections-label"></span><h2>2.3. Ordered selections<a class="headerlink" href="#ordered-selections" title="Permalink to this headline">¶</a></h2>
-<p><tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt> sorts the atoms in the
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> by atom index before returning them (this is to
+<p><code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code> sorts the atoms in the
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></code></a> by atom index before returning them (this is to
 eliminate possible duplicates in the selection). If the ordering of atoms is
 crucial (for instance when describing angles or dihedrals) or if duplicate
 atoms are required then one has to concatenate multiple AtomGroups, which does
@@ -454,7 +456,7 @@ <h3>2.2.4. Atom name selector<a class="headerlink" href="#atom-name-selector" ti
 </pre></div>
 </div>
 <p>A shortcut is to provide <em>two or more</em> selections to
-<tt class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></tt>, which then does the concatenation
+<code class="xref py py-meth docutils literal"><span class="pre">select_atoms()</span></code>, which then does the concatenation
 automatically:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="k">print</span> <span class="nb">list</span><span class="p">(</span><span class="n">universe</span><span class="o">.</span><span class="n">select_atoms</span><span class="p">(</span><span class="s">&quot;segid DMPC and resid 3 and name P&quot;</span><span class="p">,</span> <span class="s">&quot;segid DMPC and resid 2 and name P&quot;</span><span class="p">))</span>
 <span class="go">[&lt; Atom 570: name &#39;P&#39; of type &#39;180&#39; of resid &#39;DMPC&#39;, 3 and &#39;DMPC&#39;&gt;,</span>
@@ -463,10 +465,11 @@ <h3>2.2.4. Atom name selector<a class="headerlink" href="#atom-name-selector" ti
 </div>
 <p>Just for comparison to show that a single selection string does not work as one
 might expect:</p>
-<div class="highlight-python"><pre># WRONG!
-&gt;&gt;&gt; print list(universe.select_atoms("segid DMPC and ( resid 3 or resid 2 ) and name P"))
-[&lt; Atom 452: name 'P' of type '180' of resid 'DMPC', 2 and 'DMPC'&gt;,
-&lt; Atom 570: name 'P' of type '180' of resid 'DMPC', 3 and 'DMPC'&gt;]</pre>
+<div class="highlight-python"><div class="highlight"><pre># WRONG!
+&gt;&gt;&gt; print list(universe.select_atoms(&quot;segid DMPC and ( resid 3 or resid 2 ) and name P&quot;))
+[&lt; Atom 452: name &#39;P&#39; of type &#39;180&#39; of resid &#39;DMPC&#39;, 2 and &#39;DMPC&#39;&gt;,
+&lt; Atom 570: name &#39;P&#39; of type &#39;180&#39; of resid &#39;DMPC&#39;, 3 and &#39;DMPC&#39;&gt;]
+</pre></div>
 </div>
 </div>
 </div>
@@ -477,7 +480,7 @@ <h3>2.2.4. Atom name selector<a class="headerlink" href="#atom-name-selector" ti
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -492,10 +495,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="overview.html" title="1. Overview over MDAnalysis"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -505,7 +508,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections/base.html b/package/doc/html/documentation_pages/selections/base.html
index 2a9ac261ba3..b5accc04ef2 100644
--- a/package/doc/html/documentation_pages/selections/base.html
+++ b/package/doc/html/documentation_pages/selections/base.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>6.6. Base classes for the selection writers &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>6.6. Base classes for the selection writers &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="6. Selection exporters" href="../selections_modules.html" />
     <link rel="next" title="7. Core modules" href="../core_modules.html" />
     <link rel="prev" title="6.5. Jmol selections" href="jmol.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="jmol.html" title="6.5. Jmol selections"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -66,12 +64,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="../core_modules.html"
                         title="next chapter">7. Core modules</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/selections/base.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/selections/base.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,34 +90,35 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.selections.base"></span><div class="section" id="base-classes-for-the-selection-writers">
 <h1>6.6. Base classes for the selection writers<a class="headerlink" href="#base-classes-for-the-selection-writers" title="Permalink to this headline">¶</a></h1>
 <p>Specialized SelectionWriters are derived from
-<a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><tt class="xref py py-class docutils literal"><span class="pre">SelectionWriter</span></tt></a>. Override the <a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter._write_head" title="MDAnalysis.selections.base.SelectionWriter._write_head"><tt class="xref py py-meth docutils literal"><span class="pre">_write_head()</span></tt></a>,
-<a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter._translate" title="MDAnalysis.selections.base.SelectionWriter._translate"><tt class="xref py py-meth docutils literal"><span class="pre">_translate()</span></tt></a>, and <a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter._write_tail" title="MDAnalysis.selections.base.SelectionWriter._write_tail"><tt class="xref py py-meth docutils literal"><span class="pre">_write_tail()</span></tt></a>
+<a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><code class="xref py py-class docutils literal"><span class="pre">SelectionWriter</span></code></a>. Override the <a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter._write_head" title="MDAnalysis.selections.base.SelectionWriter._write_head"><code class="xref py py-meth docutils literal"><span class="pre">_write_head()</span></code></a>,
+<a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter._translate" title="MDAnalysis.selections.base.SelectionWriter._translate"><code class="xref py py-meth docutils literal"><span class="pre">_translate()</span></code></a>, and <a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter._write_tail" title="MDAnalysis.selections.base.SelectionWriter._write_tail"><code class="xref py py-meth docutils literal"><span class="pre">_write_tail()</span></code></a>
 methods.</p>
 <dl class="class">
 <dt id="MDAnalysis.selections.base.SelectionWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.selections.base.</tt><tt class="descname">SelectionWriter</tt><big>(</big><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.selections.base.</code><code class="descname">SelectionWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Export a selection in MDAnalysis to a format usable in an external package.</p>
-<p>The <a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><tt class="xref py py-class docutils literal"><span class="pre">SelectionWriter</span></tt></a> writes a selection string to a file
+<p>The <a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><code class="xref py py-class docutils literal"><span class="pre">SelectionWriter</span></code></a> writes a selection string to a file
 that can be used in another package such as <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a>, <a class="reference external" href="http://www.pymol.org/">PyMOL</a>,
 <a class="reference external" href="http://www.gromacs.org/">Gromacs</a> or <a class="reference external" href="http://www.charmm.org/">CHARMM</a>. In this way, analysis and visualization
 can be done with the best or most convenient tools at hand.</p>
-<p><a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><tt class="xref py py-class docutils literal"><span class="pre">SelectionWriter</span></tt></a> is a base class and child classes are
+<p><a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><code class="xref py py-class docutils literal"><span class="pre">SelectionWriter</span></code></a> is a base class and child classes are
 derived with the appropriate customizations for the package file
 format.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.11.0: </span>Can now also write to a <a class="reference internal" href="../lib/util.html#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><tt class="xref py py-class docutils literal"><span class="pre">NamedStream</span></tt></a> instead
-of a normal file (using <a class="reference internal" href="../lib/util.html#MDAnalysis.lib.util.openany" title="MDAnalysis.lib.util.openany"><tt class="xref py py-class docutils literal"><span class="pre">openany</span></tt></a>).</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Can now also write to a <a class="reference internal" href="../lib/util.html#MDAnalysis.lib.util.NamedStream" title="MDAnalysis.lib.util.NamedStream"><code class="xref py py-class docutils literal"><span class="pre">NamedStream</span></code></a> instead
+of a normal file (using <a class="reference internal" href="../lib/util.html#MDAnalysis.lib.util.openany" title="MDAnalysis.lib.util.openany"><code class="xref py py-class docutils literal"><span class="pre">openany</span></code></a>).</p>
+</div>
 <p>Set up for writing to <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">output file</p>
 </dd>
@@ -128,13 +129,13 @@ <h1>6.6. Base classes for the selection writers<a class="headerlink" href="#base
 <dt><em>numterms</em></dt>
 <dd><p class="first last">number of individual index numbers per line for output
 formats that write multiple entries in one line. If set
-to 0 or <tt class="docutils literal"><span class="pre">False</span></tt> then no special formatting is done  [8]</p>
+to 0 or <code class="docutils literal"><span class="pre">False</span></code> then no special formatting is done  [8]</p>
 </dd>
 <dt><em>preamble</em></dt>
 <dd><p class="first last">string that is written as a comment at the top of the file []</p>
 </dd>
 <dt><em>kwargs</em></dt>
-<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter.write" title="MDAnalysis.selections.base.SelectionWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a></p>
+<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter.write" title="MDAnalysis.selections.base.SelectionWriter.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a></p>
 </dd>
 </dl>
 </td>
@@ -143,13 +144,13 @@ <h1>6.6. Base classes for the selection writers<a class="headerlink" href="#base
 </table>
 <dl class="method">
 <dt id="MDAnalysis.selections.base.SelectionWriter.__init__">
-<tt class="descname">__init__</tt><big>(</big><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.__init__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter.__init__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__init__</code><span class="sig-paren">(</span><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.__init__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter.__init__" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set up for writing to <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">output file</p>
 </dd>
@@ -160,45 +161,13 @@ <h1>6.6. Base classes for the selection writers<a class="headerlink" href="#base
 <dt><em>numterms</em></dt>
 <dd><p class="first last">number of individual index numbers per line for output
 formats that write multiple entries in one line. If set
-to 0 or <tt class="docutils literal"><span class="pre">False</span></tt> then no special formatting is done  [8]</p>
+to 0 or <code class="docutils literal"><span class="pre">False</span></code> then no special formatting is done  [8]</p>
 </dd>
 <dt><em>preamble</em></dt>
 <dd><p class="first last">string that is written as a comment at the top of the file []</p>
 </dd>
 <dt><em>kwargs</em></dt>
-<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter.write" title="MDAnalysis.selections.base.SelectionWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a></p>
-</dd>
-</dl>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="MDAnalysis.selections.base.SelectionWriter.write">
-<tt class="descname">write</tt><big>(</big><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
-<dd><p>Write selection to the output file.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
-<dt><em>selection</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a></p>
-</dd>
-<dt><em>number</em></dt>
-<dd><p class="first last">selection will be named &#8220;mdanalysis&lt;number&gt;&#8221;
-(<tt class="docutils literal"><span class="pre">None</span></tt> auto increments between writes; useful
-when appending) [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
-</dd>
-<dt><em>name</em></dt>
-<dd><p class="first last">selection will be named <em>name</em> (instead of numbered)
-[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
-</dd>
-<dt><em>frame</em></dt>
-<dd><p class="first last">write selection of this frame (or the current one if
-<tt class="docutils literal"><span class="pre">None</span></tt> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.base.SelectionWriter.write" title="MDAnalysis.selections.base.SelectionWriter.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a></p>
 </dd>
 </dl>
 </td>
@@ -209,11 +178,11 @@ <h1>6.6. Base classes for the selection writers<a class="headerlink" href="#base
 
 <dl class="method">
 <dt id="MDAnalysis.selections.base.SelectionWriter._translate">
-<tt class="descname">_translate</tt><big>(</big><em>atoms</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter._translate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter._translate" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_translate</code><span class="sig-paren">(</span><em>atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter._translate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter._translate" title="Permalink to this definition">¶</a></dt>
 <dd><p>Translate atoms into a list of native selection terms.</p>
 <ul>
 <li><p class="first">build list of ALL selection terms as if this was a single line, e.g.
-<tt class="docutils literal"><span class="pre">['index</span> <span class="pre">12</span> <span class="pre">|',</span> <span class="pre">'index</span> <span class="pre">22</span> <span class="pre">|',</span> <span class="pre">'index</span> <span class="pre">33']</span></tt></p>
+<code class="docutils literal"><span class="pre">['index</span> <span class="pre">12</span> <span class="pre">|',</span> <span class="pre">'index</span> <span class="pre">22</span> <span class="pre">|',</span> <span class="pre">'index</span> <span class="pre">33']</span></code></p>
 </li>
 <li><p class="first">only one term per atom!!</p>
 </li>
@@ -231,31 +200,63 @@ <h1>6.6. Base classes for the selection writers<a class="headerlink" href="#base
 
 <dl class="method">
 <dt id="MDAnalysis.selections.base.SelectionWriter._write_head">
-<tt class="descname">_write_head</tt><big>(</big><em>out</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter._write_head"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter._write_head" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_write_head</code><span class="sig-paren">(</span><em>out</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter._write_head"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter._write_head" title="Permalink to this definition">¶</a></dt>
 <dd><p>Initial output to open file object <em>out</em>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.selections.base.SelectionWriter._write_tail">
-<tt class="descname">_write_tail</tt><big>(</big><em>out</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter._write_tail"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter._write_tail" title="Permalink to this definition">¶</a></dt>
+<code class="descname">_write_tail</code><span class="sig-paren">(</span><em>out</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter._write_tail"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter._write_tail" title="Permalink to this definition">¶</a></dt>
 <dd><p>Last output to open file object <em>out</em>.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.selections.base.SelectionWriter.comment">
-<tt class="descname">comment</tt><big>(</big><em>s</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.comment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">comment</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.comment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return string <em>s</em> interpolated into the comment format string.</p>
-<p>If no <tt class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></tt> is defined (None) then the
+<p>If no <code class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></code> is defined (None) then the
 empty string is returned because presumably there is no way to enter
 comments into the file.</p>
 <p>A newline is appended to non-empty strings.</p>
 </dd></dl>
 
+<dl class="method">
+<dt id="MDAnalysis.selections.base.SelectionWriter.write">
+<code class="descname">write</code><span class="sig-paren">(</span><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
+<dd><p>Write selection to the output file.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>selection</em></dt>
+<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a></p>
+</dd>
+<dt><em>number</em></dt>
+<dd><p class="first last">selection will be named &#8220;mdanalysis&lt;number&gt;&#8221;
+(<code class="docutils literal"><span class="pre">None</span></code> auto increments between writes; useful
+when appending) [<code class="docutils literal"><span class="pre">None</span></code>]</p>
+</dd>
+<dt><em>name</em></dt>
+<dd><p class="first last">selection will be named <em>name</em> (instead of numbered)
+[<code class="docutils literal"><span class="pre">None</span></code>]</p>
+</dd>
+<dt><em>frame</em></dt>
+<dd><p class="first last">write selection of this frame (or the current one if
+<code class="docutils literal"><span class="pre">None</span></code> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.selections.base.join">
-<tt class="descclassname">MDAnalysis.selections.base.</tt><tt class="descname">join</tt><big>(</big><em>seq</em>, <em>string=''</em>, <em>func=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#join"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.join" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.selections.base.</code><code class="descname">join</code><span class="sig-paren">(</span><em>seq</em>, <em>string=''</em>, <em>func=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#join"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.base.join" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a list from sequence.</p>
 <p><em>string</em> is appended to each element but the last.</p>
 <p><em>func</em> is applied to every element before appending <em>string</em>.</p>
@@ -269,7 +270,7 @@ <h1>6.6. Base classes for the selection writers<a class="headerlink" href="#base
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -284,11 +285,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="jmol.html" title="6.5. Jmol selections"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -298,7 +299,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections/charmm.html b/package/doc/html/documentation_pages/selections/charmm.html
index e52382ffc6c..ed7accf1d2d 100644
--- a/package/doc/html/documentation_pages/selections/charmm.html
+++ b/package/doc/html/documentation_pages/selections/charmm.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>6.4. CHARMM selections &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>6.4. CHARMM selections &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="6. Selection exporters" href="../selections_modules.html" />
     <link rel="next" title="6.5. Jmol selections" href="jmol.html" />
     <link rel="prev" title="6.3. Gromacs selections" href="gromacs.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="gromacs.html" title="6.3. Gromacs selections"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -66,12 +64,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="jmol.html"
                         title="next chapter">6.5. Jmol selections</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/selections/charmm.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/selections/charmm.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,24 +90,25 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.selections.charmm"></span><div class="section" id="charmm-selections">
 <h1>6.4. CHARMM selections<a class="headerlink" href="#charmm-selections" title="Permalink to this headline">¶</a></h1>
-<p>Write <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> selection to a <cite>str</cite> file
+<p>Write <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> selection to a <cite>str</cite> file
 that defines a <a class="reference external" href="http://www.charmm.org/documentation/c34b1/select.html">CHARMM selection</a>. To be used in <a class="reference external" href="http://www.charmm.org">CHARMM</a> like this:</p>
-<div class="highlight-python"><pre>stream macro.str</pre>
+<div class="highlight-python"><div class="highlight"><pre>stream macro.str
+</pre></div>
 </div>
 <p>The selection is named <em>mdanalysis001</em>.</p>
 <dl class="class">
 <dt id="MDAnalysis.selections.charmm.SelectionWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.selections.charmm.</tt><tt class="descname">SelectionWriter</tt><big>(</big><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/charmm.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.charmm.SelectionWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.selections.charmm.</code><code class="descname">SelectionWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/charmm.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.charmm.SelectionWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set up for writing to <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">output file</p>
 </dd>
@@ -118,13 +119,13 @@ <h1>6.4. CHARMM selections<a class="headerlink" href="#charmm-selections" title=
 <dt><em>numterms</em></dt>
 <dd><p class="first last">number of individual index numbers per line for output
 formats that write multiple entries in one line. If set
-to 0 or <tt class="docutils literal"><span class="pre">False</span></tt> then no special formatting is done  [8]</p>
+to 0 or <code class="docutils literal"><span class="pre">False</span></code> then no special formatting is done  [8]</p>
 </dd>
 <dt><em>preamble</em></dt>
 <dd><p class="first last">string that is written as a comment at the top of the file []</p>
 </dd>
 <dt><em>kwargs</em></dt>
-<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.charmm.SelectionWriter.write" title="MDAnalysis.selections.charmm.SelectionWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a></p>
+<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.charmm.SelectionWriter.write" title="MDAnalysis.selections.charmm.SelectionWriter.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a></p>
 </dd>
 </dl>
 </td>
@@ -133,9 +134,9 @@ <h1>6.4. CHARMM selections<a class="headerlink" href="#charmm-selections" title=
 </table>
 <dl class="method">
 <dt id="MDAnalysis.selections.charmm.SelectionWriter.comment">
-<tt class="descname">comment</tt><big>(</big><em>s</em><big>)</big><a class="headerlink" href="#MDAnalysis.selections.charmm.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">comment</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.comment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.charmm.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return string <em>s</em> interpolated into the comment format string.</p>
-<p>If no <tt class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></tt> is defined (None) then the
+<p>If no <code class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></code> is defined (None) then the
 empty string is returned because presumably there is no way to enter
 comments into the file.</p>
 <p>A newline is appended to non-empty strings.</p>
@@ -143,28 +144,28 @@ <h1>6.4. CHARMM selections<a class="headerlink" href="#charmm-selections" title=
 
 <dl class="method">
 <dt id="MDAnalysis.selections.charmm.SelectionWriter.write">
-<tt class="descname">write</tt><big>(</big><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.selections.charmm.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.charmm.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write selection to the output file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>selection</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a></p>
+<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a></p>
 </dd>
 <dt><em>number</em></dt>
 <dd><p class="first last">selection will be named &#8220;mdanalysis&lt;number&gt;&#8221;
-(<tt class="docutils literal"><span class="pre">None</span></tt> auto increments between writes; useful
-when appending) [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+(<code class="docutils literal"><span class="pre">None</span></code> auto increments between writes; useful
+when appending) [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>name</em></dt>
 <dd><p class="first last">selection will be named <em>name</em> (instead of numbered)
-[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+[<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>frame</em></dt>
 <dd><p class="first last">write selection of this frame (or the current one if
-<tt class="docutils literal"><span class="pre">None</span></tt> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<code class="docutils literal"><span class="pre">None</span></code> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -175,7 +176,7 @@ <h1>6.4. CHARMM selections<a class="headerlink" href="#charmm-selections" title=
 
 <dl class="method">
 <dt id="MDAnalysis.selections.charmm.SelectionWriter.write_preamble">
-<tt class="descname">write_preamble</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.selections.charmm.SelectionWriter.write_preamble" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_preamble</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write_preamble"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.charmm.SelectionWriter.write_preamble" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a header, depending on the file format.</p>
 </dd></dl>
 
@@ -189,7 +190,7 @@ <h1>6.4. CHARMM selections<a class="headerlink" href="#charmm-selections" title=
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -204,11 +205,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="gromacs.html" title="6.3. Gromacs selections"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -218,7 +219,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections/gromacs.html b/package/doc/html/documentation_pages/selections/gromacs.html
index 4c956b63108..f29d3917db2 100644
--- a/package/doc/html/documentation_pages/selections/gromacs.html
+++ b/package/doc/html/documentation_pages/selections/gromacs.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>6.3. Gromacs selections &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>6.3. Gromacs selections &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="6. Selection exporters" href="../selections_modules.html" />
     <link rel="next" title="6.4. CHARMM selections" href="charmm.html" />
     <link rel="prev" title="6.2. PyMOL selections" href="pymol.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="pymol.html" title="6.2. PyMOL selections"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -66,12 +64,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="charmm.html"
                         title="next chapter">6.4. CHARMM selections</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/selections/gromacs.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/selections/gromacs.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,24 +90,25 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.selections.gromacs"></span><div class="section" id="gromacs-selections">
 <h1>6.3. Gromacs selections<a class="headerlink" href="#gromacs-selections" title="Permalink to this headline">¶</a></h1>
-<p>Write <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> selection to a <a class="reference external" href="http://www.gromacs.org/Documentation/File_Formats/Index_File">ndx</a> file
+<p>Write <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> selection to a <a class="reference external" href="http://www.gromacs.org/Documentation/File_Formats/Index_File">ndx</a> file
 that defines a <a class="reference external" href="http://www.gromacs.org">Gromacs</a> index group. To be used in Gromacs like this:</p>
-<div class="highlight-python"><pre>&lt;GROMACS_COMMAND&gt; -n macro.ndx</pre>
+<div class="highlight-python"><div class="highlight"><pre>&lt;GROMACS_COMMAND&gt; -n macro.ndx
+</pre></div>
 </div>
 <p>The index groups are named <em>mdanalysis001</em>, <em>mdanalysis002</em>, etc.</p>
 <dl class="class">
 <dt id="MDAnalysis.selections.gromacs.SelectionWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.selections.gromacs.</tt><tt class="descname">SelectionWriter</tt><big>(</big><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/gromacs.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.gromacs.SelectionWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.selections.gromacs.</code><code class="descname">SelectionWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/gromacs.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.gromacs.SelectionWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set up for writing to <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">output file</p>
 </dd>
@@ -118,13 +119,13 @@ <h1>6.3. Gromacs selections<a class="headerlink" href="#gromacs-selections" titl
 <dt><em>numterms</em></dt>
 <dd><p class="first last">number of individual index numbers per line for output
 formats that write multiple entries in one line. If set
-to 0 or <tt class="docutils literal"><span class="pre">False</span></tt> then no special formatting is done  [8]</p>
+to 0 or <code class="docutils literal"><span class="pre">False</span></code> then no special formatting is done  [8]</p>
 </dd>
 <dt><em>preamble</em></dt>
 <dd><p class="first last">string that is written as a comment at the top of the file []</p>
 </dd>
 <dt><em>kwargs</em></dt>
-<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.gromacs.SelectionWriter.write" title="MDAnalysis.selections.gromacs.SelectionWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a></p>
+<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.gromacs.SelectionWriter.write" title="MDAnalysis.selections.gromacs.SelectionWriter.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a></p>
 </dd>
 </dl>
 </td>
@@ -133,9 +134,9 @@ <h1>6.3. Gromacs selections<a class="headerlink" href="#gromacs-selections" titl
 </table>
 <dl class="method">
 <dt id="MDAnalysis.selections.gromacs.SelectionWriter.comment">
-<tt class="descname">comment</tt><big>(</big><em>s</em><big>)</big><a class="headerlink" href="#MDAnalysis.selections.gromacs.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">comment</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.comment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.gromacs.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return string <em>s</em> interpolated into the comment format string.</p>
-<p>If no <tt class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></tt> is defined (None) then the
+<p>If no <code class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></code> is defined (None) then the
 empty string is returned because presumably there is no way to enter
 comments into the file.</p>
 <p>A newline is appended to non-empty strings.</p>
@@ -143,28 +144,28 @@ <h1>6.3. Gromacs selections<a class="headerlink" href="#gromacs-selections" titl
 
 <dl class="method">
 <dt id="MDAnalysis.selections.gromacs.SelectionWriter.write">
-<tt class="descname">write</tt><big>(</big><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.selections.gromacs.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.gromacs.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write selection to the output file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>selection</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a></p>
+<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a></p>
 </dd>
 <dt><em>number</em></dt>
 <dd><p class="first last">selection will be named &#8220;mdanalysis&lt;number&gt;&#8221;
-(<tt class="docutils literal"><span class="pre">None</span></tt> auto increments between writes; useful
-when appending) [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+(<code class="docutils literal"><span class="pre">None</span></code> auto increments between writes; useful
+when appending) [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>name</em></dt>
 <dd><p class="first last">selection will be named <em>name</em> (instead of numbered)
-[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+[<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>frame</em></dt>
 <dd><p class="first last">write selection of this frame (or the current one if
-<tt class="docutils literal"><span class="pre">None</span></tt> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<code class="docutils literal"><span class="pre">None</span></code> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -175,7 +176,7 @@ <h1>6.3. Gromacs selections<a class="headerlink" href="#gromacs-selections" titl
 
 <dl class="method">
 <dt id="MDAnalysis.selections.gromacs.SelectionWriter.write_preamble">
-<tt class="descname">write_preamble</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.selections.gromacs.SelectionWriter.write_preamble" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_preamble</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write_preamble"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.gromacs.SelectionWriter.write_preamble" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a header, depending on the file format.</p>
 </dd></dl>
 
@@ -189,7 +190,7 @@ <h1>6.3. Gromacs selections<a class="headerlink" href="#gromacs-selections" titl
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -204,11 +205,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="pymol.html" title="6.2. PyMOL selections"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -218,7 +219,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections/jmol.html b/package/doc/html/documentation_pages/selections/jmol.html
index ec7b2f50bb9..dbe14a1b721 100644
--- a/package/doc/html/documentation_pages/selections/jmol.html
+++ b/package/doc/html/documentation_pages/selections/jmol.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>6.5. Jmol selections &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>6.5. Jmol selections &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="6. Selection exporters" href="../selections_modules.html" />
     <link rel="next" title="6.6. Base classes for the selection writers" href="base.html" />
     <link rel="prev" title="6.4. CHARMM selections" href="charmm.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="charmm.html" title="6.4. CHARMM selections"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -66,12 +64,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="base.html"
                         title="next chapter">6.6. Base classes for the selection writers</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/selections/jmol.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/selections/jmol.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,25 +90,26 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.selections.jmol"></span><div class="section" id="jmol-selections">
 <h1>6.5. Jmol selections<a class="headerlink" href="#jmol-selections" title="Permalink to this headline">¶</a></h1>
-<p>Write <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> selection to a <cite>str</cite> file
+<p>Write <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> selection to a <cite>str</cite> file
 that defines a <a class="reference external" href="http://chemapps.stolaf.edu/jmol/docs/#define">Jmol selection</a>. To be used in <a class="reference external" href="http://wiki.jmol.org/index.php/Main_Page">Jmol</a> like this:</p>
-<div class="highlight-python"><pre>script macro.spt
-select ~selection</pre>
+<div class="highlight-python"><div class="highlight"><pre>script macro.spt
+select ~selection
+</pre></div>
 </div>
 <p>The selection is named <em>mdanalysis001</em>.TODO</p>
 <dl class="class">
 <dt id="MDAnalysis.selections.jmol.SelectionWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.selections.jmol.</tt><tt class="descname">SelectionWriter</tt><big>(</big><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/jmol.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.jmol.SelectionWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.selections.jmol.</code><code class="descname">SelectionWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/jmol.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.jmol.SelectionWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set up for writing to <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">output file</p>
 </dd>
@@ -119,13 +120,13 @@ <h1>6.5. Jmol selections<a class="headerlink" href="#jmol-selections" title="Per
 <dt><em>numterms</em></dt>
 <dd><p class="first last">number of individual index numbers per line for output
 formats that write multiple entries in one line. If set
-to 0 or <tt class="docutils literal"><span class="pre">False</span></tt> then no special formatting is done  [8]</p>
+to 0 or <code class="docutils literal"><span class="pre">False</span></code> then no special formatting is done  [8]</p>
 </dd>
 <dt><em>preamble</em></dt>
 <dd><p class="first last">string that is written as a comment at the top of the file []</p>
 </dd>
 <dt><em>kwargs</em></dt>
-<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.jmol.SelectionWriter.write" title="MDAnalysis.selections.jmol.SelectionWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a></p>
+<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.jmol.SelectionWriter.write" title="MDAnalysis.selections.jmol.SelectionWriter.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a></p>
 </dd>
 </dl>
 </td>
@@ -134,9 +135,9 @@ <h1>6.5. Jmol selections<a class="headerlink" href="#jmol-selections" title="Per
 </table>
 <dl class="method">
 <dt id="MDAnalysis.selections.jmol.SelectionWriter.comment">
-<tt class="descname">comment</tt><big>(</big><em>s</em><big>)</big><a class="headerlink" href="#MDAnalysis.selections.jmol.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">comment</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.comment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.jmol.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return string <em>s</em> interpolated into the comment format string.</p>
-<p>If no <tt class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></tt> is defined (None) then the
+<p>If no <code class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></code> is defined (None) then the
 empty string is returned because presumably there is no way to enter
 comments into the file.</p>
 <p>A newline is appended to non-empty strings.</p>
@@ -144,28 +145,28 @@ <h1>6.5. Jmol selections<a class="headerlink" href="#jmol-selections" title="Per
 
 <dl class="method">
 <dt id="MDAnalysis.selections.jmol.SelectionWriter.write">
-<tt class="descname">write</tt><big>(</big><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.selections.jmol.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.jmol.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write selection to the output file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>selection</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a></p>
+<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a></p>
 </dd>
 <dt><em>number</em></dt>
 <dd><p class="first last">selection will be named &#8220;mdanalysis&lt;number&gt;&#8221;
-(<tt class="docutils literal"><span class="pre">None</span></tt> auto increments between writes; useful
-when appending) [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+(<code class="docutils literal"><span class="pre">None</span></code> auto increments between writes; useful
+when appending) [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>name</em></dt>
 <dd><p class="first last">selection will be named <em>name</em> (instead of numbered)
-[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+[<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>frame</em></dt>
 <dd><p class="first last">write selection of this frame (or the current one if
-<tt class="docutils literal"><span class="pre">None</span></tt> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<code class="docutils literal"><span class="pre">None</span></code> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -176,7 +177,7 @@ <h1>6.5. Jmol selections<a class="headerlink" href="#jmol-selections" title="Per
 
 <dl class="method">
 <dt id="MDAnalysis.selections.jmol.SelectionWriter.write_preamble">
-<tt class="descname">write_preamble</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.selections.jmol.SelectionWriter.write_preamble" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_preamble</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write_preamble"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.jmol.SelectionWriter.write_preamble" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a header, depending on the file format.</p>
 </dd></dl>
 
@@ -190,7 +191,7 @@ <h1>6.5. Jmol selections<a class="headerlink" href="#jmol-selections" title="Per
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -205,11 +206,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="charmm.html" title="6.4. CHARMM selections"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -219,7 +220,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections/pymol.html b/package/doc/html/documentation_pages/selections/pymol.html
index 6285a0709b3..43eaa7fd759 100644
--- a/package/doc/html/documentation_pages/selections/pymol.html
+++ b/package/doc/html/documentation_pages/selections/pymol.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>6.2. PyMOL selections &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>6.2. PyMOL selections &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="6. Selection exporters" href="../selections_modules.html" />
     <link rel="next" title="6.3. Gromacs selections" href="gromacs.html" />
     <link rel="prev" title="6.1. VMD selections" href="vmd.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="vmd.html" title="6.1. VMD selections"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -66,12 +64,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="gromacs.html"
                         title="next chapter">6.3. Gromacs selections</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/selections/pymol.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/selections/pymol.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,25 +90,26 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.selections.pymol"></span><div class="section" id="pymol-selections">
 <h1>6.2. PyMOL selections<a class="headerlink" href="#pymol-selections" title="Permalink to this headline">¶</a></h1>
-<p>Write <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> selection to a
+<p>Write <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> selection to a
 script <a class="reference external" href="http://pymol.sourceforge.net/newman/user/S0210start_cmds.html#6_5_1">pml</a> file that defines <a class="reference external" href="http://www.pymol.org">PyMOL</a> atomselect macros. To be used
 in PyMOL like this:</p>
-<div class="highlight-python"><pre>@macros.pml</pre>
+<div class="highlight-python"><div class="highlight"><pre>@macros.pml
+</pre></div>
 </div>
 <p>The selections should appear in the user interface.</p>
 <dl class="class">
 <dt id="MDAnalysis.selections.pymol.SelectionWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.selections.pymol.</tt><tt class="descname">SelectionWriter</tt><big>(</big><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/pymol.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.pymol.SelectionWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.selections.pymol.</code><code class="descname">SelectionWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/pymol.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.pymol.SelectionWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set up for writing to <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">output file</p>
 </dd>
@@ -119,13 +120,13 @@ <h1>6.2. PyMOL selections<a class="headerlink" href="#pymol-selections" title="P
 <dt><em>numterms</em></dt>
 <dd><p class="first last">number of individual index numbers per line for output
 formats that write multiple entries in one line. If set
-to 0 or <tt class="docutils literal"><span class="pre">False</span></tt> then no special formatting is done  [8]</p>
+to 0 or <code class="docutils literal"><span class="pre">False</span></code> then no special formatting is done  [8]</p>
 </dd>
 <dt><em>preamble</em></dt>
 <dd><p class="first last">string that is written as a comment at the top of the file []</p>
 </dd>
 <dt><em>kwargs</em></dt>
-<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.pymol.SelectionWriter.write" title="MDAnalysis.selections.pymol.SelectionWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a></p>
+<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.pymol.SelectionWriter.write" title="MDAnalysis.selections.pymol.SelectionWriter.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a></p>
 </dd>
 </dl>
 </td>
@@ -134,9 +135,9 @@ <h1>6.2. PyMOL selections<a class="headerlink" href="#pymol-selections" title="P
 </table>
 <dl class="method">
 <dt id="MDAnalysis.selections.pymol.SelectionWriter.comment">
-<tt class="descname">comment</tt><big>(</big><em>s</em><big>)</big><a class="headerlink" href="#MDAnalysis.selections.pymol.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">comment</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.comment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.pymol.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return string <em>s</em> interpolated into the comment format string.</p>
-<p>If no <tt class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></tt> is defined (None) then the
+<p>If no <code class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></code> is defined (None) then the
 empty string is returned because presumably there is no way to enter
 comments into the file.</p>
 <p>A newline is appended to non-empty strings.</p>
@@ -144,28 +145,28 @@ <h1>6.2. PyMOL selections<a class="headerlink" href="#pymol-selections" title="P
 
 <dl class="method">
 <dt id="MDAnalysis.selections.pymol.SelectionWriter.write">
-<tt class="descname">write</tt><big>(</big><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.selections.pymol.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.pymol.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write selection to the output file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>selection</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a></p>
+<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a></p>
 </dd>
 <dt><em>number</em></dt>
 <dd><p class="first last">selection will be named &#8220;mdanalysis&lt;number&gt;&#8221;
-(<tt class="docutils literal"><span class="pre">None</span></tt> auto increments between writes; useful
-when appending) [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+(<code class="docutils literal"><span class="pre">None</span></code> auto increments between writes; useful
+when appending) [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>name</em></dt>
 <dd><p class="first last">selection will be named <em>name</em> (instead of numbered)
-[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+[<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>frame</em></dt>
 <dd><p class="first last">write selection of this frame (or the current one if
-<tt class="docutils literal"><span class="pre">None</span></tt> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<code class="docutils literal"><span class="pre">None</span></code> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -176,7 +177,7 @@ <h1>6.2. PyMOL selections<a class="headerlink" href="#pymol-selections" title="P
 
 <dl class="method">
 <dt id="MDAnalysis.selections.pymol.SelectionWriter.write_preamble">
-<tt class="descname">write_preamble</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.selections.pymol.SelectionWriter.write_preamble" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_preamble</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write_preamble"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.pymol.SelectionWriter.write_preamble" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a header, depending on the file format.</p>
 </dd></dl>
 
@@ -190,7 +191,7 @@ <h1>6.2. PyMOL selections<a class="headerlink" href="#pymol-selections" title="P
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -205,11 +206,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="vmd.html" title="6.1. VMD selections"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -219,7 +220,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections/vmd.html b/package/doc/html/documentation_pages/selections/vmd.html
index 7cf3dd26126..94229ffeae4 100644
--- a/package/doc/html/documentation_pages/selections/vmd.html
+++ b/package/doc/html/documentation_pages/selections/vmd.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>6.1. VMD selections &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>6.1. VMD selections &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="6. Selection exporters" href="../selections_modules.html" />
     <link rel="next" title="6.2. PyMOL selections" href="pymol.html" />
     <link rel="prev" title="6. Selection exporters" href="../selections_modules.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../selections_modules.html" title="6. Selection exporters"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" accesskey="U">6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -66,12 +64,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="pymol.html"
                         title="next chapter">6.2. PyMOL selections</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/selections/vmd.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/selections/vmd.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,24 +90,25 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.selections.vmd"></span><div class="section" id="vmd-selections">
 <h1>6.1. VMD selections<a class="headerlink" href="#vmd-selections" title="Permalink to this headline">¶</a></h1>
-<p>Write <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a> selection to a <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a> <cite>tcl</cite> file
+<p>Write <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a> selection to a <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a> <cite>tcl</cite> file
 that defines <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/current/ug/node120.html">atomselect macros</a>. To be used in VMD like this:</p>
-<div class="highlight-python"><pre>source macros.vmd
-set sel [atomselect top mdanalysis001]  # use macro 001</pre>
+<div class="highlight-python"><div class="highlight"><pre>source macros.vmd
+set sel [atomselect top mdanalysis001]  # use macro 001
+</pre></div>
 </div>
 <dl class="class">
 <dt id="MDAnalysis.selections.vmd.SelectionWriter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.selections.vmd.</tt><tt class="descname">SelectionWriter</tt><big>(</big><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/selections/vmd.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.vmd.SelectionWriter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.selections.vmd.</code><code class="descname">SelectionWriter</code><span class="sig-paren">(</span><em>filename</em>, <em>mode='wa'</em>, <em>numterms=None</em>, <em>preamble=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/vmd.html#SelectionWriter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.vmd.SelectionWriter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Set up for writing to <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">output file</p>
 </dd>
@@ -118,13 +119,13 @@ <h1>6.1. VMD selections<a class="headerlink" href="#vmd-selections" title="Perma
 <dt><em>numterms</em></dt>
 <dd><p class="first last">number of individual index numbers per line for output
 formats that write multiple entries in one line. If set
-to 0 or <tt class="docutils literal"><span class="pre">False</span></tt> then no special formatting is done  [8]</p>
+to 0 or <code class="docutils literal"><span class="pre">False</span></code> then no special formatting is done  [8]</p>
 </dd>
 <dt><em>preamble</em></dt>
 <dd><p class="first last">string that is written as a comment at the top of the file []</p>
 </dd>
 <dt><em>kwargs</em></dt>
-<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.vmd.SelectionWriter.write" title="MDAnalysis.selections.vmd.SelectionWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a></p>
+<dd><p class="first last">use as defaults for <a class="reference internal" href="#MDAnalysis.selections.vmd.SelectionWriter.write" title="MDAnalysis.selections.vmd.SelectionWriter.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a></p>
 </dd>
 </dl>
 </td>
@@ -133,9 +134,9 @@ <h1>6.1. VMD selections<a class="headerlink" href="#vmd-selections" title="Perma
 </table>
 <dl class="method">
 <dt id="MDAnalysis.selections.vmd.SelectionWriter.comment">
-<tt class="descname">comment</tt><big>(</big><em>s</em><big>)</big><a class="headerlink" href="#MDAnalysis.selections.vmd.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">comment</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.comment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.vmd.SelectionWriter.comment" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return string <em>s</em> interpolated into the comment format string.</p>
-<p>If no <tt class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></tt> is defined (None) then the
+<p>If no <code class="xref py py-attr docutils literal"><span class="pre">SelectionWriter.commentfmt</span></code> is defined (None) then the
 empty string is returned because presumably there is no way to enter
 comments into the file.</p>
 <p>A newline is appended to non-empty strings.</p>
@@ -143,28 +144,28 @@ <h1>6.1. VMD selections<a class="headerlink" href="#vmd-selections" title="Perma
 
 <dl class="method">
 <dt id="MDAnalysis.selections.vmd.SelectionWriter.write">
-<tt class="descname">write</tt><big>(</big><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.selections.vmd.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write</code><span class="sig-paren">(</span><em>selection</em>, <em>number=None</em>, <em>name=None</em>, <em>frame=None</em>, <em>mode=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.vmd.SelectionWriter.write" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write selection to the output file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>selection</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a></p>
+<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a></p>
 </dd>
 <dt><em>number</em></dt>
 <dd><p class="first last">selection will be named &#8220;mdanalysis&lt;number&gt;&#8221;
-(<tt class="docutils literal"><span class="pre">None</span></tt> auto increments between writes; useful
-when appending) [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+(<code class="docutils literal"><span class="pre">None</span></code> auto increments between writes; useful
+when appending) [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>name</em></dt>
 <dd><p class="first last">selection will be named <em>name</em> (instead of numbered)
-[<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+[<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>frame</em></dt>
 <dd><p class="first last">write selection of this frame (or the current one if
-<tt class="docutils literal"><span class="pre">None</span></tt> [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+<code class="docutils literal"><span class="pre">None</span></code> [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
@@ -175,7 +176,7 @@ <h1>6.1. VMD selections<a class="headerlink" href="#vmd-selections" title="Perma
 
 <dl class="method">
 <dt id="MDAnalysis.selections.vmd.SelectionWriter.write_preamble">
-<tt class="descname">write_preamble</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.selections.vmd.SelectionWriter.write_preamble" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_preamble</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/selections/base.html#SelectionWriter.write_preamble"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.selections.vmd.SelectionWriter.write_preamble" title="Permalink to this definition">¶</a></dt>
 <dd><p>Write a header, depending on the file format.</p>
 </dd></dl>
 
@@ -189,7 +190,7 @@ <h1>6.1. VMD selections<a class="headerlink" href="#vmd-selections" title="Perma
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -204,11 +205,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../selections_modules.html" title="6. Selection exporters"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../selections_modules.html" >6. Selection exporters</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -218,7 +219,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections_modules.html b/package/doc/html/documentation_pages/selections_modules.html
index 3a90f1efacc..3acee3bf025 100644
--- a/package/doc/html/documentation_pages/selections_modules.html
+++ b/package/doc/html/documentation_pages/selections_modules.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>6. Selection exporters &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>6. Selection exporters &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="6.1. VMD selections" href="selections/vmd.html" />
     <link rel="prev" title="5.22. Extensions to Bio.PDB — pdb.extensions" href="coordinates/pdbextensions.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -50,26 +48,28 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="coordinates/pdbextensions.html" title="5.22. Extensions to Bio.PDB — pdb.extensions"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../index.html">
               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="coordinates/pdbextensions.html"
-                        title="previous chapter">5.22. Extensions to <tt class="docutils literal docutils literal docutils literal"><span class="pre">Bio.PDB</span></tt> &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">pdb.extensions</span></tt></a></p>
+                        title="previous chapter">5.22. Extensions to <code class="docutils literal"><span class="pre">Bio.PDB</span></code> &#8212; <code class="docutils literal"><span class="pre">pdb.extensions</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="selections/vmd.html"
                         title="next chapter">6.1. VMD selections</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/selections_modules.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/selections_modules.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -88,21 +88,21 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="selection-exporters">
 <span id="id1"></span><h1>6. Selection exporters<a class="headerlink" href="#selection-exporters" title="Permalink to this headline">¶</a></h1>
 <p>The classes in this module allow writing a selection to a file that can be read by
 <em>another programme</em> to select the atoms in a MDAnalysis
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></tt></a>. Such cross-package interoperability
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.AtomGroup</span></code></a>. Such cross-package interoperability
 allows a user to combine their favourite tools with MDAnalysis for further
 visualization or simulation.</p>
-<p>There exist different <a class="reference internal" href="selections/base.html#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><tt class="xref py py-class docutils literal"><span class="pre">SelectionWriter</span></tt></a> classes
-for different package. The <tt class="xref py py-func docutils literal"><span class="pre">get_writer()</span></tt> function
+<p>There exist different <a class="reference internal" href="selections/base.html#MDAnalysis.selections.base.SelectionWriter" title="MDAnalysis.selections.base.SelectionWriter"><code class="xref py py-class docutils literal"><span class="pre">SelectionWriter</span></code></a> classes
+for different package. The <code class="xref py py-func docutils literal"><span class="pre">get_writer()</span></code> function
 can automatically pick the appropriate one, based on the file name extension in the
 table below.</p>
-<table border="1" class="docutils" id="supported-selection-exporters">
-<caption>Table of supported exporters and recognized file name extensions.</caption>
+<table border="1" class="docutils" id="id2">
+<span id="supported-selection-exporters"></span><caption><span class="caption-text">Table of supported exporters and recognized file name extensions.</span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
 <colgroup>
 <col width="19%" />
 <col width="14%" />
@@ -121,31 +121,31 @@ <h3>Quick search</h3>
 <td>tcl</td>
 <td>w</td>
 <td><a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a> macros, available in Representations;
-module <a class="reference internal" href="selections/vmd.html#module-MDAnalysis.selections.vmd" title="MDAnalysis.selections.vmd"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.selections.vmd</span></tt></a></td>
+module <a class="reference internal" href="selections/vmd.html#module-MDAnalysis.selections.vmd" title="MDAnalysis.selections.vmd"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.selections.vmd</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>pymol</td>
 <td>pml</td>
 <td>w</td>
 <td>simple <a class="reference external" href="http://www.pymol.org">PyMOL</a> selection string;
-module <a class="reference internal" href="selections/pymol.html#module-MDAnalysis.selections.pymol" title="MDAnalysis.selections.pymol"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.selections.pymol</span></tt></a></td>
+module <a class="reference internal" href="selections/pymol.html#module-MDAnalysis.selections.pymol" title="MDAnalysis.selections.pymol"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.selections.pymol</span></code></a></td>
 </tr>
 <tr class="row-even"><td>gromacs</td>
 <td>ndx</td>
 <td>w</td>
 <td><a class="reference external" href="http://www.gromacs.org">Gromacs</a> index file;
-module <a class="reference internal" href="selections/gromacs.html#module-MDAnalysis.selections.gromacs" title="MDAnalysis.selections.gromacs"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.selections.gromacs</span></tt></a></td>
+module <a class="reference internal" href="selections/gromacs.html#module-MDAnalysis.selections.gromacs" title="MDAnalysis.selections.gromacs"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.selections.gromacs</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>charmm</td>
 <td>str</td>
 <td>w</td>
 <td><a class="reference external" href="http://www.charmm.org">CHARMM</a> selection of individual atoms;
-module <a class="reference internal" href="selections/charmm.html#module-MDAnalysis.selections.charmm" title="MDAnalysis.selections.charmm"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.selections.charmm</span></tt></a></td>
+module <a class="reference internal" href="selections/charmm.html#module-MDAnalysis.selections.charmm" title="MDAnalysis.selections.charmm"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.selections.charmm</span></code></a></td>
 </tr>
 <tr class="row-even"><td>jmol</td>
 <td>spt</td>
 <td>w</td>
 <td><a class="reference external" href="http://wiki.jmol.org/">Jmol</a> selection commands;
-module <a class="reference internal" href="selections/jmol.html#module-MDAnalysis.selections.jmol" title="MDAnalysis.selections.jmol"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.selections.jmol</span></tt></a></td>
+module <a class="reference internal" href="selections/jmol.html#module-MDAnalysis.selections.jmol" title="MDAnalysis.selections.jmol"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.selections.jmol</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -168,7 +168,7 @@ <h3>Quick search</h3>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -183,10 +183,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="coordinates/pdbextensions.html" title="5.22. Extensions to Bio.PDB — pdb.extensions"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -196,7 +196,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/CRDParser.html b/package/doc/html/documentation_pages/topology/CRDParser.html
index 2a18f61eb3d..d4bf2b38d5e 100644
--- a/package/doc/html/documentation_pages/topology/CRDParser.html
+++ b/package/doc/html/documentation_pages/topology/CRDParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.4. CRD topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.4. CRD topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.5. GRO topology parser" href="GROParser.html" />
     <link rel="prev" title="4.3. AMBER PRMTOP topology parser" href="TOPParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="TOPParser.html" title="4.3. AMBER PRMTOP topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -74,12 +72,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="GROParser.html"
                         title="next chapter">4.5. GRO topology parser</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/CRDParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/CRDParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,7 +98,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.CRDParser"></span><div class="section" id="crd-topology-parser">
 <h1>4.4. CRD topology parser<a class="headerlink" href="#crd-topology-parser" title="Permalink to this headline">¶</a></h1>
@@ -108,21 +108,21 @@ <h1>4.4. CRD topology parser<a class="headerlink" href="#crd-topology-parser" ti
 <h2>4.4.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.CRDParser.CRDParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.CRDParser.</tt><tt class="descname">CRDParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/CRDParser.html#CRDParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.CRDParser.</code><code class="descname">CRDParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/CRDParser.html#CRDParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse a CHARMM CARD coordinate file for topology information.</p>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -138,114 +138,122 @@ <h2>4.4.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.CRDParser.CRDParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.CRDParser.CRDParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.CRDParser.CRDParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.CRDParser.CRDParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.CRDParser.CRDParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.CRDParser.CRDParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.CRDParser.CRDParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.CRDParser.CRDParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.CRDParser.CRDParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.CRDParser.CRDParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/CRDParser.html#CRDParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/CRDParser.html#CRDParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.CRDParser.CRDParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse CRD file <em>filename</em> and return the dict <cite>structure</cite>.</p>
 <p>Only reads the list of atoms.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">The <em>structure</em> dict is defined in
 <cite>MDAnalysis.topology</cite></p>
@@ -263,7 +271,7 @@ <h2>4.4.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -278,11 +286,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="TOPParser.html" title="4.3. AMBER PRMTOP topology parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -292,7 +300,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/DLPolyParser.html b/package/doc/html/documentation_pages/topology/DLPolyParser.html
index 9e80b6acd4e..468cba33502 100644
--- a/package/doc/html/documentation_pages/topology/DLPolyParser.html
+++ b/package/doc/html/documentation_pages/topology/DLPolyParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.11. DL Poly format Topology Readers — MDAnalysis.topology.DLPolyParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.11. DL Poly format Topology Readers — MDAnalysis.topology.DLPolyParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.12. DESRES Molecular Structure file format topology parser" href="DMSParser.html" />
     <link rel="prev" title="4.10. PQR topology parser" href="PQRParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="PQRParser.html" title="4.10. PQR topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -66,12 +64,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="DMSParser.html"
                         title="next chapter">4.12. DESRES Molecular Structure file format topology parser</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/DLPolyParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/DLPolyParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,10 +90,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.DLPolyParser"></span><div class="section" id="dl-poly-format-topology-readers-mdanalysis-topology-dlpolyparser">
-<h1>4.11. DL Poly format Topology Readers &#8212; <a class="reference internal" href="#module-MDAnalysis.topology.DLPolyParser" title="MDAnalysis.topology.DLPolyParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></tt></a><a class="headerlink" href="#dl-poly-format-topology-readers-mdanalysis-topology-dlpolyparser" title="Permalink to this headline">¶</a></h1>
+<h1>4.11. DL Poly format Topology Readers &#8212; <a class="reference internal" href="#module-MDAnalysis.topology.DLPolyParser" title="MDAnalysis.topology.DLPolyParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></code></a><a class="headerlink" href="#dl-poly-format-topology-readers-mdanalysis-topology-dlpolyparser" title="Permalink to this headline">¶</a></h1>
 <p>Read DL <a class="reference external" href="http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/44516.aspx">Poly</a> format topology files</p>
 </div>
 
@@ -103,7 +103,7 @@ <h1>4.11. DL Poly format Topology Readers &#8212; <a class="reference internal"
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -118,11 +118,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="PQRParser.html" title="4.10. PQR topology parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -132,7 +132,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/DMSParser.html b/package/doc/html/documentation_pages/topology/DMSParser.html
index 9861806442d..ca110086a01 100644
--- a/package/doc/html/documentation_pages/topology/DMSParser.html
+++ b/package/doc/html/documentation_pages/topology/DMSParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.12. DESRES Molecular Structure file format topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.12. DESRES Molecular Structure file format topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.13. Gromacs portable run input TPR format parser" href="TPRParser.html" />
     <link rel="prev" title="4.11. DL Poly format Topology Readers — MDAnalysis.topology.DLPolyParser" href="DLPolyParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="DLPolyParser.html" title="4.11. DL Poly format Topology Readers — MDAnalysis.topology.DLPolyParser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -70,16 +68,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="DLPolyParser.html"
-                        title="previous chapter">4.11. DL Poly format Topology Readers &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></tt></a></p>
+                        title="previous chapter">4.11. DL Poly format Topology Readers &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="TPRParser.html"
                         title="next chapter">4.13. Gromacs portable run input TPR format parser</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/DMSParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/DMSParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,7 +98,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.DMSParser"></span><div class="section" id="desres-molecular-structure-file-format-topology-parser">
 <h1>4.12. DESRES Molecular Structure file format topology parser<a class="headerlink" href="#desres-molecular-structure-file-format-topology-parser" title="Permalink to this headline">¶</a></h1>
@@ -108,7 +108,7 @@ <h1>4.12. DESRES Molecular Structure file format topology parser<a class="header
 <h2>4.12.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.DMSParser.DMSParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.DMSParser.</tt><tt class="descname">DMSParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/DMSParser.html#DMSParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.DMSParser.</code><code class="descname">DMSParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/DMSParser.html#DMSParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read a topology from a <a class="reference external" href="http://www.deshawresearch.com">DESRES</a> Molecular Structure file.</p>
 <p>Format (<a class="reference external" href="http://www.deshawresearch.com/Desmond_Users_Guide-0.7.pdf">DMS</a>) coordinate files (as used by the <a class="reference external" href="http://www.deshawresearch.com/resources_desmond.html">Desmond</a> MD package).</p>
 <p>Standard arguments for a TopologyReader:</p>
@@ -116,14 +116,14 @@ <h2>4.12.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -139,118 +139,126 @@ <h2>4.12.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.DMSParser.DMSParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.DMSParser.DMSParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.DMSParser.DMSParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.DMSParser.DMSParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.DMSParser.DMSParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.DMSParser.DMSParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.DMSParser.DMSParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.DMSParser.DMSParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.DMSParser.DMSParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.DMSParser.DMSParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/DMSParser.html#DMSParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/DMSParser.html#DMSParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.DMSParser.DMSParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse DMS file <em>filename</em> and return the dict <cite>structure</cite>.</p>
 <p>Only reads the list of atoms.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict, which contains
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict, which contains
 Atom and Bond objects</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">The <em>structure</em> dict is defined in
-<tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology</span></tt>.</p>
+<code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology</span></code>.</p>
 </div>
 </dd></dl>
 
@@ -265,7 +273,7 @@ <h2>4.12.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -280,11 +288,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="DLPolyParser.html" title="4.11. DL Poly format Topology Readers — MDAnalysis.topology.DLPolyParser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -294,7 +302,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/ExtendedPDBParser.html b/package/doc/html/documentation_pages/topology/ExtendedPDBParser.html
index 549f2dd1f15..848ab35e902 100644
--- a/package/doc/html/documentation_pages/topology/ExtendedPDBParser.html
+++ b/package/doc/html/documentation_pages/topology/ExtendedPDBParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.8. Extended PDB topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.8. Extended PDB topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.9. PDBQT topology parser" href="PDBQTParser.html" />
     <link rel="prev" title="4.7. Primitive PDB topology parser" href="PrimitivePDBParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="PrimitivePDBParser.html" title="4.7. Primitive PDB topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -74,12 +72,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="PDBQTParser.html"
                         title="next chapter">4.9. PDBQT topology parser</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/ExtendedPDBParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/ExtendedPDBParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,15 +98,16 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.ExtendedPDBParser"></span><div class="section" id="extended-pdb-topology-parser">
 <h1>4.8. Extended PDB topology parser<a class="headerlink" href="#extended-pdb-topology-parser" title="Permalink to this headline">¶</a></h1>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
 <p>This topology parser uses a PDB file to build a minimum internal structure
 representation (list of atoms). The only difference from
-<a class="reference internal" href="PrimitivePDBParser.html#module-MDAnalysis.topology.PrimitivePDBParser" title="MDAnalysis.topology.PrimitivePDBParser"><tt class="xref py py-mod docutils literal"><span class="pre">PrimitivePDBParser</span></tt></a> is that this parser reads a
+<a class="reference internal" href="PrimitivePDBParser.html#module-MDAnalysis.topology.PrimitivePDBParser" title="MDAnalysis.topology.PrimitivePDBParser"><code class="xref py py-mod docutils literal"><span class="pre">PrimitivePDBParser</span></code></a> is that this parser reads a
 non-standard PDB-like format in which residue numbers can be five digits
 instead of four.</p>
 <p>The topology reader reads a PDB file line by line and ignores atom numbers but
@@ -118,42 +119,43 @@ <h1>4.8. Extended PDB topology parser<a class="headerlink" href="#extended-pdb-t
 <p class="last">The parser processes atoms and their names. Masses are guessed and set to 0
 if unknown. Partial charges are not set.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <ul class="last simple">
-<li><a class="reference internal" href="PrimitivePDBParser.html#module-MDAnalysis.topology.PrimitivePDBParser" title="MDAnalysis.topology.PrimitivePDBParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PrimitivePDBParser</span></tt></a></li>
-<li><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.ExtendedPDBReader</span></tt></li>
-<li><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Universe</span></tt></a></li>
+<li><a class="reference internal" href="PrimitivePDBParser.html#module-MDAnalysis.topology.PrimitivePDBParser" title="MDAnalysis.topology.PrimitivePDBParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PrimitivePDBParser</span></code></a></li>
+<li><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.ExtendedPDBReader</span></code></li>
+<li><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Universe</span></code></a></li>
 </ul>
 </div>
 <div class="section" id="classes">
 <h2>4.8.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.ExtendedPDBParser.</tt><tt class="descname">ExtendedPDBParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/ExtendedPDBParser.html#ExtendedPDBParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.ExtendedPDBParser.</code><code class="descname">ExtendedPDBParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/ExtendedPDBParser.html#ExtendedPDBParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parser that obtains a list of atoms from an non-standard &#8220;extended&#8221; PDB file.</p>
 <p>Extended PDB files (MDAnalysis format specifier <em>XPDB</em>) may contain residue
 sequence numbers up to 99,999 by utilizing the insertion character field of
 the PDB standard.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.ExtendedPDBReader</span></tt></p>
+<p class="last"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.ExtendedPDBReader</span></code></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -169,118 +171,126 @@ <h2>4.8.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse atom information from PDB file <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">The <em>structure</em> dict is defined in
 <cite>MDAnalysis.topology</cite> and the file is
 read with
-<a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.PrimitivePDBReader</span></tt></a>.</p>
+<a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.PrimitivePDBReader</span></code></a>.</p>
 </div>
 </dd></dl>
 
@@ -295,7 +305,7 @@ <h2>4.8.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -310,11 +320,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="PrimitivePDBParser.html" title="4.7. Primitive PDB topology parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -324,7 +334,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/GMSParser.html b/package/doc/html/documentation_pages/topology/GMSParser.html
index 8b9f5cab750..d2ea949025d 100644
--- a/package/doc/html/documentation_pages/topology/GMSParser.html
+++ b/package/doc/html/documentation_pages/topology/GMSParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.17. GAMESS Topology Parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.17. GAMESS Topology Parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
-    <link rel="next" title="4.18. Base topology reader classes — MDAnalysis.topology.base" href="base.html" />
+    <link rel="next" title="4.18. HOOMD XML topology parser" href="HoomdXMLParser.html" />
     <link rel="prev" title="4.16. LAMMPSParser" href="LAMMPSParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -46,16 +44,16 @@ <h3>Navigation</h3>
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="base.html" title="4.18. Base topology reader classes — MDAnalysis.topology.base"
+          <a href="HoomdXMLParser.html" title="4.18. HOOMD XML topology parser"
              accesskey="N">next</a> |</li>
         <li class="right" >
           <a href="LAMMPSParser.html" title="4.16. LAMMPSParser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -72,14 +70,16 @@ <h4>Previous topic</h4>
   <p class="topless"><a href="LAMMPSParser.html"
                         title="previous chapter">4.16. LAMMPSParser</a></p>
   <h4>Next topic</h4>
-  <p class="topless"><a href="base.html"
-                        title="next chapter">4.18. Base topology reader classes &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.topology.base</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/GMSParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <p class="topless"><a href="HoomdXMLParser.html"
+                        title="next chapter">4.18. HOOMD XML topology parser</a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/GMSParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,12 +98,13 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.GMSParser"></span><div class="section" id="gamess-topology-parser">
 <h1>4.17. GAMESS Topology Parser<a class="headerlink" href="#gamess-topology-parser" title="Permalink to this headline">¶</a></h1>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.1.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.1.</span></p>
+</div>
 <p>Reads a <a class="reference external" href="http://www.msg.ameslab.gov/gamess/">GAMESS</a> output file (also <a class="reference external" href="http://classic.chem.msu.su/gran/gamess/index.html">Firefly</a> and <a class="reference external" href="http://www.cfs.dl.ac.uk/">GAMESS-UK</a>) and pulls
 element information from it.  Symmetrical assembly is read (not
 symmetry element!).  Atom names are read from the GAMESS section.  Any
@@ -112,23 +113,24 @@ <h1>4.17. GAMESS Topology Parser<a class="headerlink" href="#gamess-topology-par
 <h2>4.17.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.GMSParser.GMSParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.GMSParser.</tt><tt class="descname">GMSParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/GMSParser.html#GMSParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.GMSParser.</code><code class="descname">GMSParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/GMSParser.html#GMSParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser" title="Permalink to this definition">¶</a></dt>
 <dd><p><a class="reference external" href="http://www.msg.ameslab.gov/gamess/">GAMESS</a> topology parser.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.1.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.1.</span></p>
+</div>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -144,103 +146,111 @@ <h2>4.17.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.GMSParser.GMSParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GMSParser.GMSParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GMSParser.GMSParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GMSParser.GMSParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GMSParser.GMSParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GMSParser.GMSParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GMSParser.GMSParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GMSParser.GMSParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GMSParser.GMSParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GMSParser.GMSParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/GMSParser.html#GMSParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/GMSParser.html#GMSParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.GMSParser.GMSParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read list of atoms from a GAMESS file.</p>
 </dd></dl>
 
@@ -255,7 +265,7 @@ <h2>4.17.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -265,16 +275,16 @@ <h3>Navigation</h3>
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="base.html" title="4.18. Base topology reader classes — MDAnalysis.topology.base"
+          <a href="HoomdXMLParser.html" title="4.18. HOOMD XML topology parser"
              >next</a> |</li>
         <li class="right" >
           <a href="LAMMPSParser.html" title="4.16. LAMMPSParser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -284,7 +294,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/GROParser.html b/package/doc/html/documentation_pages/topology/GROParser.html
index acc5062bd4f..6e7732eb3c0 100644
--- a/package/doc/html/documentation_pages/topology/GROParser.html
+++ b/package/doc/html/documentation_pages/topology/GROParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.5. GRO topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.5. GRO topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.6. PDB topology parser" href="PDBParser.html" />
     <link rel="prev" title="4.4. CRD topology parser" href="CRDParser.html" /> 
   </head>
-  <body>
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
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@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="CRDParser.html" title="4.4. CRD topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
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-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -74,12 +72,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="PDBParser.html"
                         title="next chapter">4.6. PDB topology parser</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/GROParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/GROParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,35 +98,35 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.GROParser"></span><div class="section" id="gro-topology-parser">
 <h1>4.5. GRO topology parser<a class="headerlink" href="#gro-topology-parser" title="Permalink to this headline">¶</a></h1>
 <p>Read a list of atoms from a GROMOS/Gromacs GRO coordinate file to
 build a basic topology.</p>
 <p>Atom types, masses and charges are guessed.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../coordinates/GRO.html#module-MDAnalysis.coordinates.GRO" title="MDAnalysis.coordinates.GRO"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></tt></a></p>
+<p class="last"><a class="reference internal" href="../coordinates/GRO.html#module-MDAnalysis.coordinates.GRO" title="MDAnalysis.coordinates.GRO"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.GRO</span></code></a></p>
 </div>
 <div class="section" id="classes">
 <h2>4.5.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.GROParser.GROParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.GROParser.</tt><tt class="descname">GROParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/GROParser.html#GROParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.GROParser.</code><code class="descname">GROParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/GROParser.html#GROParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -142,117 +142,125 @@ <h2>4.5.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.GROParser.GROParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GROParser.GROParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GROParser.GROParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GROParser.GROParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GROParser.GROParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GROParser.GROParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GROParser.GROParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GROParser.GROParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GROParser.GROParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.GROParser.GROParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/GROParser.html#GROParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/GROParser.html#GROParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.GROParser.GROParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse GRO file <em>filename</em> and return the dict <cite>structure</cite>.</p>
 <p>Only reads the list of atoms.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">The <em>structure</em> dict is defined in
-<a class="reference internal" href="base.html#module-MDAnalysis.topology.base" title="MDAnalysis.topology.base"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.base()</span></tt></a>.</p>
+<a class="reference internal" href="base.html#module-MDAnalysis.topology.base" title="MDAnalysis.topology.base"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.base()</span></code></a>.</p>
 </div>
 </dd></dl>
 
@@ -267,7 +275,7 @@ <h2>4.5.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -282,11 +290,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="CRDParser.html" title="4.4. CRD topology parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -296,7 +304,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/HoomdXMLParser.html b/package/doc/html/documentation_pages/topology/HoomdXMLParser.html
index 5000103fb21..7e89a4c5a24 100644
--- a/package/doc/html/documentation_pages/topology/HoomdXMLParser.html
+++ b/package/doc/html/documentation_pages/topology/HoomdXMLParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.18. HOOMD XML topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.18. HOOMD XML topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.19. Base topology reader classes — MDAnalysis.topology.base" href="base.html" />
     <link rel="prev" title="4.17. GAMESS Topology Parser" href="GMSParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="GMSParser.html" title="4.17. GAMESS Topology Parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -73,13 +71,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">4.17. GAMESS Topology Parser</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="base.html"
-                        title="next chapter">4.19. Base topology reader classes &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.topology.base</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/HoomdXMLParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">4.19. Base topology reader classes &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology.base</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/HoomdXMLParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,13 +98,14 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.HoomdXMLParser"></span><div class="section" id="hoomd-xml-topology-parser">
 <h1>4.18. HOOMD XML topology parser<a class="headerlink" href="#hoomd-xml-topology-parser" title="Permalink to this headline">¶</a></h1>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
-<p>The <a class="reference internal" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser" title="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser"><tt class="xref py py-class docutils literal"><span class="pre">HoomdXMLParser</span></tt></a> generates a topology from files for the <a class="reference external" href="http://codeblue.umich.edu/hoomd-blue/index.html">HOOMD</a> code.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
+</div>
+<p>The <a class="reference internal" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser" title="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser"><code class="xref py py-class docutils literal"><span class="pre">HoomdXMLParser</span></code></a> generates a topology from files for the <a class="reference external" href="http://codeblue.umich.edu/hoomd-blue/index.html">HOOMD</a> code.</p>
 <p>Read a list of atoms from a <a class="reference external" href="http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html">HOOMD XML</a> file to build a basic topology.
 Atom names are set to atom type if not present (which they probably aren&#8217;t).
 Elements are guessed based on atom types.
@@ -116,20 +117,20 @@ <h1>4.18. HOOMD XML topology parser<a class="headerlink" href="#hoomd-xml-topolo
 <h2>4.18.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.HoomdXMLParser.</tt><tt class="descname">HoomdXMLParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/HoomdXMLParser.html#HoomdXMLParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.HoomdXMLParser.</code><code class="descname">HoomdXMLParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/HoomdXMLParser.html#HoomdXMLParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -145,103 +146,111 @@ <h2>4.18.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/HoomdXMLParser.html#HoomdXMLParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/HoomdXMLParser.html#HoomdXMLParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse Hoomd XML file <em>filename</em> and return the dict <cite>structure</cite>.</p>
 <p>Hoomd XML format does not contain a node for names. The parser will
 look for a name node anyway, and if it doesn&#8217;t find one, it will use
@@ -255,17 +264,18 @@ <h2>4.18.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">The <em>structure</em> dict is defined in
-<a class="reference internal" href="base.html#module-MDAnalysis.topology.base" title="MDAnalysis.topology.base"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.base()</span></tt></a>.</p>
+<a class="reference internal" href="base.html#module-MDAnalysis.topology.base" title="MDAnalysis.topology.base"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.base()</span></code></a>.</p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.11.0.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.11.0.</span></p>
 </dd></dl>
 
 </dd></dl>
@@ -279,7 +289,7 @@ <h2>4.18.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -294,11 +304,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="GMSParser.html" title="4.17. GAMESS Topology Parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -308,7 +318,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/LAMMPSParser.html b/package/doc/html/documentation_pages/topology/LAMMPSParser.html
index 76d66951c5c..70a99a91657 100644
--- a/package/doc/html/documentation_pages/topology/LAMMPSParser.html
+++ b/package/doc/html/documentation_pages/topology/LAMMPSParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.16. LAMMPSParser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.16. LAMMPSParser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.17. GAMESS Topology Parser" href="GMSParser.html" />
     <link rel="prev" title="4.15. XYZ Topology Parser" href="XYZParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="XYZParser.html" title="4.15. XYZ Topology Parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -75,12 +73,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="GMSParser.html"
                         title="next chapter">4.17. GAMESS Topology Parser</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/LAMMPSParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/LAMMPSParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -99,17 +99,17 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.LAMMPSParser"></span><div class="section" id="lammpsparser">
 <h1>4.16. LAMMPSParser<a class="headerlink" href="#lammpsparser" title="Permalink to this headline">¶</a></h1>
-<p>The <tt class="xref py py-func docutils literal"><span class="pre">parse()</span></tt> function reads a <a class="reference external" href="http://lammps.sandia.gov/">LAMMPS</a> data file to build a system
+<p>The <code class="xref py py-func docutils literal"><span class="pre">parse()</span></code> function reads a <a class="reference external" href="http://lammps.sandia.gov/">LAMMPS</a> data file to build a system
 topology.</p>
 <div class="section" id="classes">
 <h2>4.16.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.LAMMPSParser.</tt><tt class="descname">DATAParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#DATAParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.LAMMPSParser.</code><code class="descname">DATAParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#DATAParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse a LAMMPS DATA file for topology and coordinates.</p>
 <p>Note that <a class="reference external" href="http://lammps.sandia.gov/">LAMMPS</a> DATA files can be used standalone.</p>
 <p>Both topology and coordinate parsing functionality is kept in this
@@ -118,21 +118,22 @@ <h2>4.16.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 <p>The parser implements the <a class="reference external" href=":http://lammps.sandia.gov/doc/2001/data_format.html">LAMMPS DATA file format</a> but only for
 the LAMMPS <a class="reference external" href="http://lammps.sandia.gov/doc/atom_style.html">atom_style</a> <em>full</em> (numeric ids 7, 10) and
 <em>molecular</em> (6, 9).</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -148,109 +149,117 @@ <h2>4.16.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#DATAParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#DATAParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parses a <a class="reference external" href="http://lammps.sandia.gov/">LAMMPS</a> DATA file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict.</td>
 </tr>
 </tbody>
 </table>
@@ -258,7 +267,7 @@ <h2>4.16.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.DATAParser.read_DATA_timestep">
-<tt class="descname">read_DATA_timestep</tt><big>(</big><em>n_atoms</em>, <em>TS_class</em>, <em>TS_kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#DATAParser.read_DATA_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.read_DATA_timestep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">read_DATA_timestep</code><span class="sig-paren">(</span><em>n_atoms</em>, <em>TS_class</em>, <em>TS_kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#DATAParser.read_DATA_timestep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.DATAParser.read_DATA_timestep" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read a DATA file and try and extract x, v, box.</p>
 <ul class="simple">
 <li>positions</li>
@@ -266,8 +275,9 @@ <h2>4.16.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 <li>box information</li>
 </ul>
 <p>Fills this into the Timestep object and returns it</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
 </dd></dl>
 
 </dd></dl>
@@ -277,10 +287,10 @@ <h2>4.16.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 <h2>4.16.2. Deprecated classes<a class="headerlink" href="#deprecated-classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.LAMMPSParser.</tt><tt class="descname">LAMMPSDataConverter</tt><big>(</big><em>filename=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#LAMMPSDataConverter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.LAMMPSParser.</code><code class="descname">LAMMPSDataConverter</code><span class="sig-paren">(</span><em>filename=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#LAMMPSDataConverter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter" title="Permalink to this definition">¶</a></dt>
 <dd><p>Class to parse a <a class="reference external" href="http://lammps.sandia.gov/">LAMMPS</a> DATA file and convert it to PSF/PDB.</p>
 <p>The DATA file contains both topology and coordinate information.</p>
-<p>The <a class="reference internal" href="#MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter" title="MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter"><tt class="xref py py-class docutils literal"><span class="pre">LAMMPSDataConverter</span></tt></a> class can extract topology information and
+<p>The <a class="reference internal" href="#MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter" title="MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter"><code class="xref py py-class docutils literal"><span class="pre">LAMMPSDataConverter</span></code></a> class can extract topology information and
 coordinates from a <a class="reference external" href="http://lammps.sandia.gov/">LAMMPS</a> data file. For instance, in order to
 produce a PSF file of the topology and a PDB file of the coordinates
 from a data file &#8220;lammps.data&#8221; you can use:</p>
@@ -291,23 +301,25 @@ <h2>4.16.2. Deprecated classes<a class="headerlink" href="#deprecated-classes" t
 </pre></div>
 </div>
 <p>You can then read a trajectory (e.g. a LAMMPS DCD, see
-<a class="reference internal" href="../coordinates/LAMMPS.html#MDAnalysis.coordinates.LAMMPS.DCDReader" title="MDAnalysis.coordinates.LAMMPS.DCDReader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS.DCDReader</span></tt></a>) with</p>
+<a class="reference internal" href="../coordinates/LAMMPS.html#MDAnalysis.coordinates.LAMMPS.DCDReader" title="MDAnalysis.coordinates.LAMMPS.DCDReader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.LAMMPS.DCDReader</span></code></a>) with</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="n">u</span> <span class="o">=</span> <span class="n">MDAnalysis</span><span class="o">.</span><span class="n">Unverse</span><span class="p">(</span><span class="s">&quot;lammps.psf&quot;</span><span class="p">,</span> <span class="s">&quot;lammps.dcd&quot;</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="s">&quot;LAMMPS&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
-<p class="deprecated">
-<span class="versionmodified">Deprecated since version 0.9.0.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Renamed from <tt class="docutils literal"><span class="pre">LAMMPSData</span></tt> to <tt class="docutils literal"><span class="pre">LAMMPSDataConverter</span></tt>.</p>
+<div class="deprecated">
+<p><span class="versionmodified">Deprecated since version 0.9.0.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Renamed from <code class="docutils literal"><span class="pre">LAMMPSData</span></code> to <code class="docutils literal"><span class="pre">LAMMPSDataConverter</span></code>.</p>
+</div>
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter.writePDB">
-<tt class="descname">writePDB</tt><big>(</big><em>filename</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#LAMMPSDataConverter.writePDB"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter.writePDB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">writePDB</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#LAMMPSDataConverter.writePDB"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter.writePDB" title="Permalink to this definition">¶</a></dt>
 <dd><p>Export coordinates to a simple PDB file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter.writePSF">
-<tt class="descname">writePSF</tt><big>(</big><em>filename</em>, <em>names=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#LAMMPSDataConverter.writePSF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter.writePSF" title="Permalink to this definition">¶</a></dt>
+<code class="descname">writePSF</code><span class="sig-paren">(</span><em>filename</em>, <em>names=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/LAMMPSParser.html#LAMMPSDataConverter.writePSF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter.writePSF" title="Permalink to this definition">¶</a></dt>
 <dd><p>Export topology information to a simple PSF file.</p>
 </dd></dl>
 
@@ -322,7 +334,7 @@ <h2>4.16.2. Deprecated classes<a class="headerlink" href="#deprecated-classes" t
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -337,11 +349,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="XYZParser.html" title="4.15. XYZ Topology Parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -351,7 +363,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/MOL2Parser.html b/package/doc/html/documentation_pages/topology/MOL2Parser.html
index 646feac4183..1783148eda7 100644
--- a/package/doc/html/documentation_pages/topology/MOL2Parser.html
+++ b/package/doc/html/documentation_pages/topology/MOL2Parser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.14. MOL2 file format — MDAnalysis.coordinates.MOL2 &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.14. MOL2 file format — MDAnalysis.coordinates.MOL2 &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.15. XYZ Topology Parser" href="XYZParser.html" />
     <link rel="prev" title="4.13. Gromacs portable run input TPR format parser" href="TPRParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="TPRParser.html" title="4.13. Gromacs portable run input TPR format parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">4.14. MOL2 file format &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></tt></a><ul>
+<li><a class="reference internal" href="#">4.14. MOL2 file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></code></a><ul>
 <li><a class="reference internal" href="#classes">4.14.1. Classes</a></li>
 </ul>
 </li>
@@ -74,12 +72,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="XYZParser.html"
                         title="next chapter">4.15. XYZ Topology Parser</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/MOL2Parser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/MOL2Parser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,33 +98,34 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.MOL2Parser"></span><div class="section" id="mol2-file-format-mdanalysis-coordinates-mol2">
-<h1>4.14. MOL2 file format &#8212; <a class="reference internal" href="../coordinates/MOL2.html#module-MDAnalysis.coordinates.MOL2" title="MDAnalysis.coordinates.MOL2"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></tt></a><a class="headerlink" href="#mol2-file-format-mdanalysis-coordinates-mol2" title="Permalink to this headline">¶</a></h1>
+<h1>4.14. MOL2 file format &#8212; <a class="reference internal" href="../coordinates/MOL2.html#module-MDAnalysis.coordinates.MOL2" title="MDAnalysis.coordinates.MOL2"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></code></a><a class="headerlink" href="#mol2-file-format-mdanalysis-coordinates-mol2" title="Permalink to this headline">¶</a></h1>
 <p>Classes to read <a class="reference external" href="http://www.tripos.com/">Tripos</a> molecule structure format (<a class="reference external" href="http://www.tripos.com/data/support/mol2.pdf">MOL2</a>) coordinate
 and topology files. Used by the <a class="reference external" href="http://dock.compbio.ucsf.edu/">DOCK</a> docking code.</p>
 <div class="section" id="classes">
 <h2>4.14.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.MOL2Parser.MOL2Parser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.MOL2Parser.</tt><tt class="descname">MOL2Parser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/MOL2Parser.html#MOL2Parser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.MOL2Parser.</code><code class="descname">MOL2Parser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/MOL2Parser.html#MOL2Parser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read topology from a <a class="reference external" href="http://www.tripos.com/">Tripos</a> <a class="reference external" href="http://www.tripos.com/data/support/mol2.pdf">MOL2</a> file.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9: </span>Now subclasses TopologyReader</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9: </span>Now subclasses TopologyReader</p>
+</div>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -140,117 +141,125 @@ <h2>4.14.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.MOL2Parser.MOL2Parser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.MOL2Parser.MOL2Parser.parse">
-<tt class="descname">parse</tt><big>(</big><em>filename=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/MOL2Parser.html#MOL2Parser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><em>filename=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/MOL2Parser.html#MOL2Parser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.MOL2Parser.MOL2Parser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse MOL2 file <em>filename</em> and return the dict <cite>structure</cite>.</p>
 <p>Only reads the list of atoms.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">The <em>structure</em> dict is defined in
-<a class="reference internal" href="PSFParser.html#MDAnalysis.topology.PSFParser.PSFParser" title="MDAnalysis.topology.PSFParser.PSFParser"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.PSFParser.PSFParser()</span></tt></a>.</p>
+<a class="reference internal" href="PSFParser.html#MDAnalysis.topology.PSFParser.PSFParser" title="MDAnalysis.topology.PSFParser.PSFParser"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.PSFParser.PSFParser()</span></code></a>.</p>
 </div>
 </dd></dl>
 
@@ -265,7 +274,7 @@ <h2>4.14.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -280,11 +289,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="TPRParser.html" title="4.13. Gromacs portable run input TPR format parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -294,7 +303,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/PDBParser.html b/package/doc/html/documentation_pages/topology/PDBParser.html
index bfdcbd0bc90..cfa4148a764 100644
--- a/package/doc/html/documentation_pages/topology/PDBParser.html
+++ b/package/doc/html/documentation_pages/topology/PDBParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.6. PDB topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.6. PDB topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.7. Primitive PDB topology parser" href="PrimitivePDBParser.html" />
     <link rel="prev" title="4.5. GRO topology parser" href="GROParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="GROParser.html" title="4.5. GRO topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -74,12 +72,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="PrimitivePDBParser.html"
                         title="next chapter">4.7. Primitive PDB topology parser</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/PDBParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/PDBParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,7 +98,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.PDBParser"></span><div class="section" id="pdb-topology-parser">
 <h1>4.6. PDB topology parser<a class="headerlink" href="#pdb-topology-parser" title="Permalink to this headline">¶</a></h1>
@@ -109,13 +109,13 @@ <h1>4.6. PDB topology parser<a class="headerlink" href="#pdb-topology-parser" ti
 (partial) charges are deduced. Masses are guessed and set to
 0 if unknown.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../coordinates/PDB.html#module-MDAnalysis.coordinates.PDB" title="MDAnalysis.coordinates.PDB"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></tt></a> and <tt class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></tt></p>
+<p class="last"><a class="reference internal" href="../coordinates/PDB.html#module-MDAnalysis.coordinates.PDB" title="MDAnalysis.coordinates.PDB"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></code></a> and <code class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></code></p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="PrimitivePDBParser.html#module-MDAnalysis.topology.PrimitivePDBParser" title="MDAnalysis.topology.PrimitivePDBParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PrimitivePDBParser</span></tt></a> (which
+<p class="last"><a class="reference internal" href="PrimitivePDBParser.html#module-MDAnalysis.topology.PrimitivePDBParser" title="MDAnalysis.topology.PrimitivePDBParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PrimitivePDBParser</span></code></a> (which
 <em>can</em> guess conectivity but does not support all subleties of the full
 PDB format)</p>
 </div>
@@ -123,21 +123,21 @@ <h1>4.6. PDB topology parser<a class="headerlink" href="#pdb-topology-parser" ti
 <h2>4.6.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.PDBParser.PDBParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.PDBParser.</tt><tt class="descname">PDBParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/PDBParser.html#PDBParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.PDBParser.</code><code class="descname">PDBParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/PDBParser.html#PDBParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read minimum topology information from a PDB file.</p>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -153,116 +153,124 @@ <h2>4.6.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBParser.PDBParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBParser.PDBParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBParser.PDBParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBParser.PDBParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBParser.PDBParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBParser.PDBParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBParser.PDBParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBParser.PDBParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBParser.PDBParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBParser.PDBParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/PDBParser.html#PDBParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/PDBParser.html#PDBParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PDBParser.PDBParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse atom information from PDB file <em>pdbfile</em>.</p>
 <p>Only reads the list of atoms.</p>
-<p>This functions uses the <tt class="xref py py-class docutils literal"><span class="pre">Bio.PDB.PDBParser</span></tt> as used by
-<a class="reference internal" href="../coordinates/pdbextensions.html#MDAnalysis.coordinates.pdb.extensions.get_structure" title="MDAnalysis.coordinates.pdb.extensions.get_structure"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.coordinates.pdb.extensions.get_structure()</span></tt></a>.</p>
+<p>This functions uses the <code class="xref py py-class docutils literal"><span class="pre">Bio.PDB.PDBParser</span></code> as used by
+<a class="reference internal" href="../coordinates/pdbextensions.html#MDAnalysis.coordinates.pdb.extensions.get_structure" title="MDAnalysis.coordinates.pdb.extensions.get_structure"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.coordinates.pdb.extensions.get_structure()</span></code></a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">The <em>structure</em> dict is defined in <cite>MDAnalysis.topology</cite>.</p>
 </div>
@@ -279,7 +287,7 @@ <h2>4.6.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -294,11 +302,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="GROParser.html" title="4.5. GRO topology parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -308,7 +316,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/PDBQTParser.html b/package/doc/html/documentation_pages/topology/PDBQTParser.html
index 2b6d1aee41e..64a51a1e6ff 100644
--- a/package/doc/html/documentation_pages/topology/PDBQTParser.html
+++ b/package/doc/html/documentation_pages/topology/PDBQTParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.9. PDBQT topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.9. PDBQT topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.10. PQR topology parser" href="PQRParser.html" />
     <link rel="prev" title="4.8. Extended PDB topology parser" href="ExtendedPDBParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="ExtendedPDBParser.html" title="4.8. Extended PDB topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -74,12 +72,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="PQRParser.html"
                         title="next chapter">4.10. PQR topology parser</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/PDBQTParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/PDBQTParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,13 +98,13 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.PDBQTParser"></span><div class="section" id="pdbqt-topology-parser">
 <h1>4.9. PDBQT topology parser<a class="headerlink" href="#pdbqt-topology-parser" title="Permalink to this headline">¶</a></h1>
 <p>Use a <a class="reference external" href="http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file">PDBQT</a> file to build a minimum internal structure representation (list of
-atoms), including <a class="reference external" href="http://autodock.scripps.edu/">AutoDock</a> atom types (stored as <tt class="xref py py-attr docutils literal"><span class="pre">Atom.type</span></tt>) and
-partial charges (<tt class="xref py py-attr docutils literal"><span class="pre">Atom.charge</span></tt>).</p>
+atoms), including <a class="reference external" href="http://autodock.scripps.edu/">AutoDock</a> atom types (stored as <code class="xref py py-attr docutils literal"><span class="pre">Atom.type</span></code>) and
+partial charges (<code class="xref py py-attr docutils literal"><span class="pre">Atom.charge</span></code>).</p>
 <ul class="simple">
 <li>Reads a PDBQT file line by line and does not require sequential atom numbering.</li>
 <li>Multi-model PDBQT files are not supported.</li>
@@ -114,7 +114,7 @@ <h1>4.9. PDBQT topology parser<a class="headerlink" href="#pdbqt-topology-parser
 <p class="last">Only reads atoms and their names; connectivity is not
 deduced. Masses are guessed and set to 0 if unknown.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last"><cite>MDAnalysis.coordinates.PDBQT</cite></p>
 </div>
@@ -122,21 +122,21 @@ <h1>4.9. PDBQT topology parser<a class="headerlink" href="#pdbqt-topology-parser
 <h2>4.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.PDBQTParser.PDBQTParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.PDBQTParser.</tt><tt class="descname">PDBQTParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/PDBQTParser.html#PDBQTParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.PDBQTParser.</code><code class="descname">PDBQTParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/PDBQTParser.html#PDBQTParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read topology from a PDBQT file.</p>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -152,118 +152,126 @@ <h2>4.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBQTParser.PDBQTParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PDBQTParser.PDBQTParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/PDBQTParser.html#PDBQTParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/PDBQTParser.html#PDBQTParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PDBQTParser.PDBQTParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse atom information from PDBQT file <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">The <em>structure</em> dict is defined in
-<a class="reference internal" href="PSFParser.html#MDAnalysis.topology.PSFParser.PSFParser" title="MDAnalysis.topology.PSFParser.PSFParser"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.PSFParser.PSFParser()</span></tt></a> and the file
+<a class="reference internal" href="PSFParser.html#MDAnalysis.topology.PSFParser.PSFParser" title="MDAnalysis.topology.PSFParser.PSFParser"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.PSFParser.PSFParser()</span></code></a> and the file
 is read with
-<a class="reference internal" href="../coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTReader" title="MDAnalysis.coordinates.PDBQT.PDBQTReader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDBQT.PDBQTReader</span></tt></a>.</p>
+<a class="reference internal" href="../coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTReader" title="MDAnalysis.coordinates.PDBQT.PDBQTReader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDBQT.PDBQTReader</span></code></a>.</p>
 </div>
 </dd></dl>
 
@@ -278,7 +286,7 @@ <h2>4.9.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -293,11 +301,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="ExtendedPDBParser.html" title="4.8. Extended PDB topology parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -307,7 +315,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/PQRParser.html b/package/doc/html/documentation_pages/topology/PQRParser.html
index d35b1c52f9a..44147c49bea 100644
--- a/package/doc/html/documentation_pages/topology/PQRParser.html
+++ b/package/doc/html/documentation_pages/topology/PQRParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.10. PQR topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.10. PQR topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.11. DL Poly format Topology Readers — MDAnalysis.topology.DLPolyParser" href="DLPolyParser.html" />
     <link rel="prev" title="4.9. PDBQT topology parser" href="PDBQTParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="PDBQTParser.html" title="4.9. PDBQT topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -73,13 +71,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">4.9. PDBQT topology parser</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="DLPolyParser.html"
-                        title="next chapter">4.11. DL Poly format Topology Readers &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/PQRParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">4.11. DL Poly format Topology Readers &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/PQRParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,42 +98,43 @@ <h3>Quick search</h3>
     <div class="document">
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-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.PQRParser"></span><div class="section" id="pqr-topology-parser">
 <h1>4.10. PQR topology parser<a class="headerlink" href="#pqr-topology-parser" title="Permalink to this headline">¶</a></h1>
 <p>Read atoms with charges from a <a class="reference external" href="http://www.poissonboltzmann.org/file-formats/biomolecular-structurw/pqr">PQR</a> file (as written by <a class="reference external" href="http://www.poissonboltzmann.org/pdb2pqr">PDB2PQR</a>). No
 connectivity is deduced.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last">The file format is described in <a class="reference internal" href="../coordinates/PQR.html#module-MDAnalysis.coordinates.PQR" title="MDAnalysis.coordinates.PQR"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PQR</span></tt></a>.</p>
+<p class="last">The file format is described in <a class="reference internal" href="../coordinates/PQR.html#module-MDAnalysis.coordinates.PQR" title="MDAnalysis.coordinates.PQR"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PQR</span></code></a>.</p>
 </div>
 <div class="section" id="classes">
 <h2>4.10.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.PQRParser.PQRParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.PQRParser.</tt><tt class="descname">PQRParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/PQRParser.html#PQRParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.PQRParser.</code><code class="descname">PQRParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/PQRParser.html#PQRParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse atom information from PQR file <em>filename</em>.</p>
 <p>Only reads the list of atoms. Reads the charges and radii from the
 PQR file and populates the
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.charge" title="MDAnalysis.core.AtomGroup.Atom.charge"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.charge</span></tt></a> and
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.radius" title="MDAnalysis.core.AtomGroup.Atom.radius"><tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.radius</span></tt></a> attribute.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Read chainID from a PQR file and use it as segid (before we always used
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.charge" title="MDAnalysis.core.AtomGroup.Atom.charge"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.charge</span></code></a> and
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.radius" title="MDAnalysis.core.AtomGroup.Atom.radius"><code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Atom.radius</span></code></a> attribute.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Read chainID from a PQR file and use it as segid (before we always used
 &#8216;SYSTEM&#8217; as the new segid).</p>
+</div>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -149,117 +150,125 @@ <h2>4.10.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.PQRParser.PQRParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PQRParser.PQRParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PQRParser.PQRParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PQRParser.PQRParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PQRParser.PQRParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PQRParser.PQRParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PQRParser.PQRParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PQRParser.PQRParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PQRParser.PQRParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PQRParser.PQRParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/PQRParser.html#PQRParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/PQRParser.html#PQRParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PQRParser.PQRParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse atom information from PQR file <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">The <em>structure</em> dict is defined in
 <cite>MDAnalysis.topology</cite> and
-<a class="reference internal" href="../coordinates/PQR.html#MDAnalysis.coordinates.PQR.PQRReader" title="MDAnalysis.coordinates.PQR.PQRReader"><tt class="xref py py-class docutils literal"><span class="pre">PQRReader</span></tt></a> is used to read
+<a class="reference internal" href="../coordinates/PQR.html#MDAnalysis.coordinates.PQR.PQRReader" title="MDAnalysis.coordinates.PQR.PQRReader"><code class="xref py py-class docutils literal"><span class="pre">PQRReader</span></code></a> is used to read
 the PQR file.</p>
 </div>
 </dd></dl>
@@ -275,7 +284,7 @@ <h2>4.10.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -290,11 +299,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="PDBQTParser.html" title="4.9. PDBQT topology parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -304,7 +313,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/PSFParser.html b/package/doc/html/documentation_pages/topology/PSFParser.html
index 38fcce864ad..610a1610798 100644
--- a/package/doc/html/documentation_pages/topology/PSFParser.html
+++ b/package/doc/html/documentation_pages/topology/PSFParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.2. PSF topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.2. PSF topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
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-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.3. AMBER PRMTOP topology parser" href="TOPParser.html" />
     <link rel="prev" title="4.1. Topology readers — MDAnalysis.topology" href="init.html" /> 
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@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="init.html" title="4.1. Topology readers — MDAnalysis.topology"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
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@@ -70,16 +68,18 @@ <h3><a href="../../index.html">Table Of Contents</a></h3>
 
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+                        title="previous chapter">4.1. Topology readers &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="TOPParser.html"
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-  <h3>This Page</h3>
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-           rel="nofollow">Show Source</a></li>
-  </ul>
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+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
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+      <li><a href="../../_sources/documentation_pages/topology/PSFParser.txt"
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   <span class="target" id="module-MDAnalysis.topology.PSFParser"></span><div class="section" id="psf-topology-parser">
 <h1>4.2. PSF topology parser<a class="headerlink" href="#psf-topology-parser" title="Permalink to this headline">¶</a></h1>
@@ -111,21 +111,21 @@ <h1>4.2. PSF topology parser<a class="headerlink" href="#psf-topology-parser" ti
 <h2>4.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.PSFParser.PSFParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.PSFParser.</tt><tt class="descname">PSFParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/PSFParser.html#PSFParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.PSFParser.</code><code class="descname">PSFParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/PSFParser.html#PSFParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read topology information from a CHARMM/NAMD/XPLOR <a class="reference external" href="http://www.charmm.org/documentation/c35b1/struct.html">PSF</a> file.</p>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -141,109 +141,117 @@ <h2>4.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.PSFParser.PSFParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PSFParser.PSFParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PSFParser.PSFParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PSFParser.PSFParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PSFParser.PSFParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PSFParser.PSFParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PSFParser.PSFParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PSFParser.PSFParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PSFParser.PSFParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PSFParser.PSFParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/PSFParser.html#PSFParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/PSFParser.html#PSFParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PSFParser.PSFParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse PSF file <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict as defined here.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict as defined here.</td>
 </tr>
 </tbody>
 </table>
@@ -260,7 +268,7 @@ <h2>4.2.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -275,11 +283,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="init.html" title="4.1. Topology readers — MDAnalysis.topology"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -289,7 +297,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/PrimitivePDBParser.html b/package/doc/html/documentation_pages/topology/PrimitivePDBParser.html
index 972bef31786..0af9343244a 100644
--- a/package/doc/html/documentation_pages/topology/PrimitivePDBParser.html
+++ b/package/doc/html/documentation_pages/topology/PrimitivePDBParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.7. Primitive PDB topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.7. Primitive PDB topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.8. Extended PDB topology parser" href="ExtendedPDBParser.html" />
     <link rel="prev" title="4.6. PDB topology parser" href="PDBParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="PDBParser.html" title="4.6. PDB topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -74,12 +72,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="ExtendedPDBParser.html"
                         title="next chapter">4.8. Extended PDB topology parser</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/PrimitivePDBParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/PrimitivePDBParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,7 +98,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.PrimitivePDBParser"></span><div class="section" id="primitive-pdb-topology-parser">
 <h1>4.7. Primitive PDB topology parser<a class="headerlink" href="#primitive-pdb-topology-parser" title="Permalink to this headline">¶</a></h1>
@@ -108,46 +108,47 @@ <h1>4.7. Primitive PDB topology parser<a class="headerlink" href="#primitive-pdb
 numbers but only reads residue numbers up to 9,999 correctly. If you
 have systems containing at least 10,000 residues then you need to use
 a different file format (e.g. the &#8220;extended&#8221; PDB, <em>XPDB</em> format, see
-<a class="reference internal" href="ExtendedPDBParser.html#module-MDAnalysis.topology.ExtendedPDBParser" title="MDAnalysis.topology.ExtendedPDBParser"><tt class="xref py py-mod docutils literal"><span class="pre">ExtendedPDBParser</span></tt></a>) that can handle residue
+<a class="reference internal" href="ExtendedPDBParser.html#module-MDAnalysis.topology.ExtendedPDBParser" title="MDAnalysis.topology.ExtendedPDBParser"><code class="xref py py-mod docutils literal"><span class="pre">ExtendedPDBParser</span></code></a>) that can handle residue
 numbers up to 99,999.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The parser processes atoms and their names. Masses are guessed and set to 0
 if unknown. Partial charges are not set.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <ul class="last simple">
-<li><a class="reference internal" href="ExtendedPDBParser.html#module-MDAnalysis.topology.ExtendedPDBParser" title="MDAnalysis.topology.ExtendedPDBParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.ExtendedPDBParser</span></tt></a></li>
-<li><a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.PrimitivePDBReader</span></tt></a></li>
-<li><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Universe</span></tt></a></li>
+<li><a class="reference internal" href="ExtendedPDBParser.html#module-MDAnalysis.topology.ExtendedPDBParser" title="MDAnalysis.topology.ExtendedPDBParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.ExtendedPDBParser</span></code></a></li>
+<li><a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.PrimitivePDBReader</span></code></a></li>
+<li><a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.core.AtomGroup.Universe</span></code></a></li>
 </ul>
 </div>
 <div class="section" id="classes">
 <h2>4.7.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.PrimitivePDBParser.</tt><tt class="descname">PrimitivePDBParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/PrimitivePDBParser.html#PrimitivePDBParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.PrimitivePDBParser.</code><code class="descname">PrimitivePDBParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/PrimitivePDBParser.html#PrimitivePDBParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parser that obtains a list of atoms from a standard PDB file.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.PrimitivePDBReader</span></tt></a></p>
+<p class="last"><a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.PrimitivePDBReader</span></code></a></p>
+</div>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
 </div>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -163,118 +164,126 @@ <h2>4.7.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/PrimitivePDBParser.html#PrimitivePDBParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/PrimitivePDBParser.html#PrimitivePDBParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse atom information from PDB file <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last">The <em>structure</em> dict is defined in
 <cite>MDAnalysis.topology</cite> and the file is
 read with
-<a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.PrimitivePDBReader</span></tt></a>.</p>
+<a class="reference internal" href="../coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="MDAnalysis.coordinates.PDB.PrimitivePDBReader"><code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.PDB.PrimitivePDBReader</span></code></a>.</p>
 </div>
 </dd></dl>
 
@@ -289,7 +298,7 @@ <h2>4.7.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -304,11 +313,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="PDBParser.html" title="4.6. PDB topology parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -318,7 +327,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/TOPParser.html b/package/doc/html/documentation_pages/topology/TOPParser.html
index 07f45273a55..b589d4fc3ec 100644
--- a/package/doc/html/documentation_pages/topology/TOPParser.html
+++ b/package/doc/html/documentation_pages/topology/TOPParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.3. AMBER PRMTOP topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.3. AMBER PRMTOP topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
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       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
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     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.4. CRD topology parser" href="CRDParser.html" />
     <link rel="prev" title="4.2. PSF topology parser" href="PSFParser.html" /> 
   </head>
-  <body>
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
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       <ul>
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@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="PSFParser.html" title="4.2. PSF topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
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@@ -74,12 +72,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
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+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
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+      <li><a href="../../_sources/documentation_pages/topology/TOPParser.txt"
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   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
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@@ -98,7 +98,7 @@ <h3>Quick search</h3>
     <div class="document">
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-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.TOPParser"></span><div class="section" id="amber-prmtop-topology-parser">
 <h1>4.3. AMBER PRMTOP topology parser<a class="headerlink" href="#amber-prmtop-topology-parser" title="Permalink to this headline">¶</a></h1>
@@ -117,7 +117,7 @@ <h1>4.3. AMBER PRMTOP topology parser<a class="headerlink" href="#amber-prmtop-t
 <h2>4.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.TOPParser.TOPParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.TOPParser.</tt><tt class="descname">TOPParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/TOPParser.html#TOPParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.TOPParser.</code><code class="descname">TOPParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/TOPParser.html#TOPParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reads topology information from an AMBER top file.</p>
 <blockquote>
 <div><p>It uses atom types, partial charges and masses from the PRMTOP
@@ -126,21 +126,22 @@ <h2>4.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 specification</a>.  The reader tries to detect if it is a newer
 (AMBER 12?) file format by looking for the flag &#8220;ATOMIC_NUMBER&#8221;.</p>
 </div></blockquote>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.6: </span>parses both amber10 and amber12 formats</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.6: </span>parses both amber10 and amber12 formats</p>
+</div>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -156,109 +157,117 @@ <h2>4.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.TOPParser.TOPParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TOPParser.TOPParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TOPParser.TOPParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TOPParser.TOPParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TOPParser.TOPParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TOPParser.TOPParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TOPParser.TOPParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TOPParser.TOPParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TOPParser.TOPParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TOPParser.TOPParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/TOPParser.html#TOPParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/TOPParser.html#TOPParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.TOPParser.TOPParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse Amber PRMTOP topology file <em>filename</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict.</td>
 </tr>
 </tbody>
 </table>
@@ -275,7 +284,7 @@ <h2>4.3.1. Classes<a class="headerlink" href="#classes" title="Permalink to this
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -290,11 +299,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="PSFParser.html" title="4.2. PSF topology parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -304,7 +313,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/TPRParser.html b/package/doc/html/documentation_pages/topology/TPRParser.html
index a0e2f801dc9..3eeea37d342 100644
--- a/package/doc/html/documentation_pages/topology/TPRParser.html
+++ b/package/doc/html/documentation_pages/topology/TPRParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.13. Gromacs portable run input TPR format parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.13. Gromacs portable run input TPR format parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.14. MOL2 file format — MDAnalysis.coordinates.MOL2" href="MOL2Parser.html" />
     <link rel="prev" title="4.12. DESRES Molecular Structure file format topology parser" href="DMSParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="DMSParser.html" title="4.12. DESRES Molecular Structure file format topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -74,13 +72,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">4.12. DESRES Molecular Structure file format topology parser</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="MOL2Parser.html"
-                        title="next chapter">4.14. MOL2 file format &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/TPRParser.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">4.14. MOL2 file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/TPRParser.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -99,19 +99,19 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.TPRParser"></span><div class="section" id="gromacs-portable-run-input-tpr-format-parser">
 <h1>4.13. Gromacs portable run input TPR format parser<a class="headerlink" href="#gromacs-portable-run-input-tpr-format-parser" title="Permalink to this headline">¶</a></h1>
-<p>The <a class="reference internal" href="#module-MDAnalysis.topology.TPRParser" title="MDAnalysis.topology.TPRParser"><tt class="xref py py-mod docutils literal"><span class="pre">TPRParser</span></tt></a> module allows reading of a
+<p>The <a class="reference internal" href="#module-MDAnalysis.topology.TPRParser" title="MDAnalysis.topology.TPRParser"><code class="xref py py-mod docutils literal"><span class="pre">TPRParser</span></code></a> module allows reading of a
 <a class="reference external" href="http://www.gromacs.org">Gromacs</a> portable run input file (a <a class="reference external" href="http://manual.gromacs.org/current/online/tpr.html">TPR file</a>). At the moment, only
 atom information is read and used to build a minimal topology. Because
 the file format of the TPR file is changing rapidly, not all versions
 are currently supported. The known working versions and the
 approximate Gromacs release numbers are listed in the table
-<a class="reference internal" href="#tpr-format-table"><em>TPR format versions</em></a>.</p>
-<table border="1" class="docutils" id="tpr-format-table">
-<caption>TPR format versions and generations read by <tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.TPRParser.parse()</span></tt>.</caption>
+<a class="reference internal" href="#tpr-format-table"><span>TPR format versions</span></a>.</p>
+<table border="1" class="docutils" id="id3">
+<span id="tpr-format-table"></span><caption><span class="caption-text">TPR format versions and generations read by <code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.TPRParser.parse()</span></code>.</span><a class="headerlink" href="#id3" title="Permalink to this table">¶</a></caption>
 <colgroup>
 <col width="20%" />
 <col width="29%" />
@@ -158,25 +158,25 @@ <h1>4.13. Gromacs portable run input TPR format parser<a class="headerlink" href
 <h2>4.13.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.TPRParser.TPRParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.TPRParser.</tt><tt class="descname">TPRParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/TPRParser.html#TPRParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser" title="Permalink to this definition">¶</a></dt>
-<dd><p>Read topology information from a <a class="reference external" href="http://www.gromacs.org">Gromacs</a> <a href="#id3"><span class="problematic" id="id4">TPR_</span></a> file.</p>
-<div class="admonition-see-also admonition seealso">
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.TPRParser.</code><code class="descname">TPRParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/TPRParser.html#TPRParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser" title="Permalink to this definition">¶</a></dt>
+<dd><p>Read topology information from a <a class="reference external" href="http://www.gromacs.org">Gromacs</a> <a href="#id4"><span class="problematic" id="id5">TPR_</span></a> file.</p>
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.TPR</span></tt></p>
+<p class="last"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.TPR</span></code></p>
 </div>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -192,109 +192,117 @@ <h2>4.13.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.TPRParser.TPRParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TPRParser.TPRParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TPRParser.TPRParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TPRParser.TPRParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TPRParser.TPRParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TPRParser.TPRParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TPRParser.TPRParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TPRParser.TPRParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TPRParser.TPRParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.TPRParser.TPRParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/TPRParser.html#TPRParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/TPRParser.html#TPRParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.TPRParser.TPRParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse a Gromacs TPR file into a MDAnalysis internal topology structure.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body"><tt class="docutils literal"><span class="pre">structure</span></tt> dict</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><code class="docutils literal"><span class="pre">structure</span></code> dict</td>
 </tr>
 </tbody>
 </table>
@@ -302,9 +310,9 @@ <h2>4.13.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 
 </dd></dl>
 
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="tpr_util.html#module-MDAnalysis.topology.tpr" title="MDAnalysis.topology.tpr"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr</span></tt></a></p>
+<p class="last"><a class="reference internal" href="tpr_util.html#module-MDAnalysis.topology.tpr" title="MDAnalysis.topology.tpr"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr</span></code></a></p>
 </div>
 </div>
 <div class="section" id="development-notes">
@@ -323,17 +331,17 @@ <h2>4.13.2. Development notes<a class="headerlink" href="#development-notes" tit
 section is actually a list of Improper Dih.</p>
 <p>This tpr parser is written according to the following files</p>
 <ul class="simple">
-<li><tt class="file docutils literal"><em><span class="pre">gromacs_dir</span></em><span class="pre">/src/kernel/gmxdump.c</span></tt></li>
-<li><tt class="file docutils literal"><em><span class="pre">gromacs_dir</span></em><span class="pre">/src/gmxlib/tpxio.c</span></tt> (the most important one)</li>
-<li><tt class="file docutils literal"><em><span class="pre">gromacs_dir</span></em><span class="pre">/src/gmxlib/gmxfio_rw.c</span></tt></li>
-<li><tt class="file docutils literal"><em><span class="pre">gromacs_dir</span></em><span class="pre">/src/gmxlib/gmxfio_xdr.c</span></tt></li>
-<li><tt class="file docutils literal"><em><span class="pre">gromacs_dir</span></em><span class="pre">/include/gmxfiofio.h</span></tt></li>
+<li><code class="file docutils literal"><em><span class="pre">gromacs_dir</span></em><span class="pre">/src/kernel/gmxdump.c</span></code></li>
+<li><code class="file docutils literal"><em><span class="pre">gromacs_dir</span></em><span class="pre">/src/gmxlib/tpxio.c</span></code> (the most important one)</li>
+<li><code class="file docutils literal"><em><span class="pre">gromacs_dir</span></em><span class="pre">/src/gmxlib/gmxfio_rw.c</span></code></li>
+<li><code class="file docutils literal"><em><span class="pre">gromacs_dir</span></em><span class="pre">/src/gmxlib/gmxfio_xdr.c</span></code></li>
+<li><code class="file docutils literal"><em><span class="pre">gromacs_dir</span></em><span class="pre">/include/gmxfiofio.h</span></code></li>
 </ul>
-<p>The function <tt class="xref py py-func docutils literal"><span class="pre">read_tpxheader()</span></tt> is based on the
+<p>The function <code class="xref py py-func docutils literal"><span class="pre">read_tpxheader()</span></code> is based on the
 <a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/wiki/TPRReaderDevelopment">TPRReaderDevelopment</a> notes.  Functions with names starting with
-<tt class="docutils literal"><span class="pre">read_</span></tt> or <tt class="docutils literal"><span class="pre">do_</span></tt> are trying to be similar to those in
-<tt class="file docutils literal"><span class="pre">gmxdump.c</span></tt> or <tt class="file docutils literal"><span class="pre">tpxio.c</span></tt>, those with <tt class="docutils literal"><span class="pre">extract_</span></tt> are new.</p>
-<p>Wherever <tt class="docutils literal"><span class="pre">fver_err(fver)</span></tt> is used, it means the tpx version problem
+<code class="docutils literal"><span class="pre">read_</span></code> or <code class="docutils literal"><span class="pre">do_</span></code> are trying to be similar to those in
+<code class="file docutils literal"><span class="pre">gmxdump.c</span></code> or <code class="file docutils literal"><span class="pre">tpxio.c</span></code>, those with <code class="docutils literal"><span class="pre">extract_</span></code> are new.</p>
+<p>Wherever <code class="docutils literal"><span class="pre">fver_err(fver)</span></code> is used, it means the tpx version problem
 haven&#8217;t be resolved for those other than 58 and 73 (or gromacs version
 before 4.x)</p>
 </div>
@@ -345,7 +353,7 @@ <h2>4.13.2. Development notes<a class="headerlink" href="#development-notes" tit
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
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@@ -360,11 +368,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="DMSParser.html" title="4.12. DESRES Molecular Structure file format topology parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -374,7 +382,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/XYZParser.html b/package/doc/html/documentation_pages/topology/XYZParser.html
index 1109702b63a..086e33dde54 100644
--- a/package/doc/html/documentation_pages/topology/XYZParser.html
+++ b/package/doc/html/documentation_pages/topology/XYZParser.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.15. XYZ Topology Parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.15. XYZ Topology Parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
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+        VERSION:     '0.11.0',
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         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
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-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
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     <link rel="next" title="4.16. LAMMPSParser" href="LAMMPSParser.html" />
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+    <div class="related" role="navigation" aria-label="related navigation">
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         <li class="right" >
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              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
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+                        title="previous chapter">4.14. MOL2 file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></code></a></p>
   <h4>Next topic</h4>
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-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-           rel="nofollow">Show Source</a></li>
-  </ul>
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+  <div role="note" aria-label="source link">
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   <span class="target" id="module-MDAnalysis.topology.XYZParser"></span><div class="section" id="xyz-topology-parser">
 <h1>4.15. XYZ Topology Parser<a class="headerlink" href="#xyz-topology-parser" title="Permalink to this headline">¶</a></h1>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.1.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.1.</span></p>
+</div>
 <p>Reads an xyz file and pulls the atom information from it.  Because
 xyz only has atom name information, all information about residues
 and segments won&#8217;t be populated.</p>
@@ -111,23 +112,24 @@ <h1>4.15. XYZ Topology Parser<a class="headerlink" href="#xyz-topology-parser" t
 <h2>4.15.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.XYZParser.XYZParser">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.XYZParser.</tt><tt class="descname">XYZParser</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/XYZParser.html#XYZParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.XYZParser.</code><code class="descname">XYZParser</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/XYZParser.html#XYZParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>Parse a list of atoms from an XYZ file.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.1.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.1.</span></p>
+</div>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -143,109 +145,117 @@ <h2>4.15.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.XYZParser.XYZParser.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.XYZParser.XYZParser.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.XYZParser.XYZParser.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.XYZParser.XYZParser.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.XYZParser.XYZParser.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.XYZParser.XYZParser.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.XYZParser.XYZParser.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.XYZParser.XYZParser.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.XYZParser.XYZParser.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.XYZParser.XYZParser.parse">
-<tt class="descname">parse</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/XYZParser.html#XYZParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">parse</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/XYZParser.html#XYZParser.parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.XYZParser.XYZParser.parse" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the file and return the structure.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">MDAnalysis internal <em>structure</em> dict.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MDAnalysis internal <em>structure</em> dict.</td>
 </tr>
 </tbody>
 </table>
@@ -262,7 +272,7 @@ <h2>4.15.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -277,11 +287,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="MOL2Parser.html" title="4.14. MOL2 file format — MDAnalysis.coordinates.MOL2"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -291,7 +301,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/base.html b/package/doc/html/documentation_pages/topology/base.html
index 06acd8d61d3..e182b424d68 100644
--- a/package/doc/html/documentation_pages/topology/base.html
+++ b/package/doc/html/documentation_pages/topology/base.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.19. Base topology reader classes — MDAnalysis.topology.base &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.19. Base topology reader classes — MDAnalysis.topology.base &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.20. Common functions for topology building — MDAnalysis.topology.core" href="core.html" />
     <link rel="prev" title="4.18. HOOMD XML topology parser" href="HoomdXMLParser.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="HoomdXMLParser.html" title="4.18. HOOMD XML topology parser"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">4.19. Base topology reader classes &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.topology.base</span></tt></a><ul>
+<li><a class="reference internal" href="#">4.19. Base topology reader classes &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology.base</span></code></a><ul>
 <li><a class="reference internal" href="#classes">4.19.1. Classes</a></li>
 </ul>
 </li>
@@ -73,13 +71,15 @@ <h4>Previous topic</h4>
                         title="previous chapter">4.18. HOOMD XML topology parser</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="core.html"
-                        title="next chapter">4.20. Common functions for topology building &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.topology.core</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/base.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">4.20. Common functions for topology building &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology.core</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/base.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -98,18 +98,18 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.base"></span><div class="section" id="base-topology-reader-classes-mdanalysis-topology-base">
-<h1>4.19. Base topology reader classes &#8212; <a class="reference internal" href="#module-MDAnalysis.topology.base" title="MDAnalysis.topology.base"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.base</span></tt></a><a class="headerlink" href="#base-topology-reader-classes-mdanalysis-topology-base" title="Permalink to this headline">¶</a></h1>
+<h1>4.19. Base topology reader classes &#8212; <a class="reference internal" href="#module-MDAnalysis.topology.base" title="MDAnalysis.topology.base"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.base</span></code></a><a class="headerlink" href="#base-topology-reader-classes-mdanalysis-topology-base" title="Permalink to this headline">¶</a></h1>
 <p>Derive topology reader classes from the base class in this module. All
-topology readers raise <tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> upon failing to read a topology
-file and <tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> upon failing to make sense of the read data.</p>
+topology readers raise <code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> upon failing to read a topology
+file and <code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> upon failing to make sense of the read data.</p>
 <div class="section" id="classes">
 <h2>4.19.1. Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.base.TopologyReader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.base.</tt><tt class="descname">TopologyReader</tt><big>(</big><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/base.html#TopologyReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.base.</code><code class="descname">TopologyReader</code><span class="sig-paren">(</span><em>filename</em>, <em>universe=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/base.html#TopologyReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader" title="Permalink to this definition">¶</a></dt>
 <dd><p>Base class for topology readers</p>
 <dl class="docutils">
 <dt>All topology readers must:</dt>
@@ -123,31 +123,33 @@ <h2>4.19.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><ul class="first last simple">
-<li><tt class="xref py py-exc docutils literal"><span class="pre">IOError</span></tt> upon failing to read a topology file</li>
-<li><tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> upon failing to make sense of the read data</li>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><ul class="first last simple">
+<li><code class="xref py py-exc docutils literal"><span class="pre">IOError</span></code> upon failing to read a topology file</li>
+<li><code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> upon failing to make sense of the read data</li>
 </ul>
 </td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.2: </span>Added keyword &#8216;universe&#8217; to pass to Atom creation.</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.2: </span>Added keyword &#8216;universe&#8217; to pass to Atom creation.</p>
+</div>
 <p>Standard arguments for a TopologyReader:</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><dl class="first docutils">
 <dt><em>filename</em></dt>
 <dd><p class="first last">name of the topology file</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first last docutils">
+<tr class="field-even field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first last docutils">
 <dt><em>universe</em></dt>
 <dd><p class="first last">Supply a Universe to the Parser.  This then passes it to the
 atom instances that are created within parsers.</p>
@@ -163,98 +165,106 @@ <h2>4.19.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
 </table>
 <dl class="method">
 <dt id="MDAnalysis.topology.base.TopologyReader.close">
-<tt class="descname">close</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.close" title="Permalink to this definition">¶</a></dt>
 <dd><p>Close the trajectory file.</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.base.TopologyReader.convert_forces_from_native">
-<tt class="descname">convert_forces_from_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_from_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_forces_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of forces array <em>force</em> from native units to base units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.base.TopologyReader.convert_forces_to_native">
-<tt class="descname">convert_forces_to_native</tt><big>(</big><em>force</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_forces_to_native</code><span class="sig-paren">(</span><em>force</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_forces_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of force array <em>force</em> from base units to native units.</p>
 <p>By default, the input <em>force</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.base.TopologyReader.convert_pos_from_native">
-<tt class="descname">convert_pos_from_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_from_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_pos_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array x from native units to base units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.base.TopologyReader.convert_pos_to_native">
-<tt class="descname">convert_pos_to_native</tt><big>(</big><em>x</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_pos_to_native</code><span class="sig-paren">(</span><em>x</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_pos_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Conversion of coordinate array x from base units to native units.</p>
 <p>By default, the input <em>x</em> is modified in place and also returned.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.base.TopologyReader.convert_time_from_native">
-<tt class="descname">convert_time_from_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_from_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_time_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from native units to base units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned (although note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.base.TopologyReader.convert_time_to_native">
-<tt class="descname">convert_time_to_native</tt><big>(</big><em>t</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_time_to_native</code><span class="sig-paren">(</span><em>t</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_time_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert time <em>t</em> from base units to native units.</p>
 <p>By default, the input <em>t</em> is modified in place and also
 returned. (Also note that scalar values <em>t</em> are passed by
 value in Python and hence an in-place modification has no
 effect on the caller.)</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <tt class="docutils literal"><span class="pre">False</span></tt> so that a
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.7.5: </span>Keyword <em>inplace</em> can be set to <code class="docutils literal"><span class="pre">False</span></code> so that a
 modified copy is returned <em>unless</em> no conversion takes
 place, in which case the reference to the unmodified <em>x</em> is
 returned.</p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.base.TopologyReader.convert_velocities_from_native">
-<tt class="descname">convert_velocities_from_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_from_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_velocities_from_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of velocities array <em>v</em> from native units to base units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.base.TopologyReader.convert_velocities_to_native">
-<tt class="descname">convert_velocities_to_native</tt><big>(</big><em>v</em>, <em>inplace=True</em><big>)</big><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_velocities_to_native</code><span class="sig-paren">(</span><em>v</em>, <em>inplace=True</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.base.TopologyReader.convert_velocities_to_native" title="Permalink to this definition">¶</a></dt>
 <dd><p>In-place conversion of coordinate array <em>v</em> from base units to native units.</p>
 <p>By default, the input <em>v</em> is modified in place and also returned.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.5.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.5.</span></p>
+</div>
 </dd></dl>
 
 </dd></dl>
@@ -268,7 +278,7 @@ <h2>4.19.1. Classes<a class="headerlink" href="#classes" title="Permalink to thi
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -283,11 +293,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="HoomdXMLParser.html" title="4.18. HOOMD XML topology parser"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -297,7 +307,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/core.html b/package/doc/html/documentation_pages/topology/core.html
index db0de091793..9b8de1ab938 100644
--- a/package/doc/html/documentation_pages/topology/core.html
+++ b/package/doc/html/documentation_pages/topology/core.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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@@ -8,7 +6,7 @@
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+    <title>4.20. Common functions for topology building — MDAnalysis.topology.core &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
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+          title="Search within MDAnalysis 0.11.0 documentation"
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-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
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   <span class="target" id="module-MDAnalysis.topology.core"></span><div class="section" id="common-functions-for-topology-building-mdanalysis-topology-core">
-<h1>4.20. Common functions for topology building &#8212; <a class="reference internal" href="#module-MDAnalysis.topology.core" title="MDAnalysis.topology.core"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.core</span></tt></a><a class="headerlink" href="#common-functions-for-topology-building-mdanalysis-topology-core" title="Permalink to this headline">¶</a></h1>
+<h1>4.20. Common functions for topology building &#8212; <a class="reference internal" href="#module-MDAnalysis.topology.core" title="MDAnalysis.topology.core"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.core</span></code></a><a class="headerlink" href="#common-functions-for-topology-building-mdanalysis-topology-core" title="Permalink to this headline">¶</a></h1>
 <p>The various topology parsers make use of functions and classes in this
 module. They are mostly of use to developers.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="tables.html#module-MDAnalysis.topology.tables" title="MDAnalysis.topology.tables"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tables</span></tt></a> for some hard-coded atom
-information that is used by functions such as <a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_type" title="MDAnalysis.topology.core.guess_atom_type"><tt class="xref py py-func docutils literal"><span class="pre">guess_atom_type()</span></tt></a> and
-<a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_mass" title="MDAnalysis.topology.core.guess_atom_mass"><tt class="xref py py-func docutils literal"><span class="pre">guess_atom_mass()</span></tt></a>.</p>
+<p class="last"><a class="reference internal" href="tables.html#module-MDAnalysis.topology.tables" title="MDAnalysis.topology.tables"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tables</span></code></a> for some hard-coded atom
+information that is used by functions such as <a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_type" title="MDAnalysis.topology.core.guess_atom_type"><code class="xref py py-func docutils literal"><span class="pre">guess_atom_type()</span></code></a> and
+<a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_mass" title="MDAnalysis.topology.core.guess_atom_mass"><code class="xref py py-func docutils literal"><span class="pre">guess_atom_mass()</span></code></a>.</p>
 </div>
 <dl class="function">
 <dt id="MDAnalysis.topology.core.build_residues">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">build_residues</tt><big>(</big><em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#build_residues"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.build_residues" title="Permalink to this definition">¶</a></dt>
-<dd><p>Create a list <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> instances from
-a list of <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances.</p>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">build_residues</code><span class="sig-paren">(</span><em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#build_residues"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.build_residues" title="Permalink to this definition">¶</a></dt>
+<dd><p>Create a list <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> instances from
+a list of <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances.</p>
 <p>Updating residues also changes the underlying
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances, which record
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances, which record
 to which residue an atom belongs.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">List of <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a> instances</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">List of <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a> instances</td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Now allows resids to be given in non sequential order</p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Now allows resids to be given in non sequential order</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.core.build_segments">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">build_segments</tt><big>(</big><em>atoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#build_segments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.build_segments" title="Permalink to this definition">¶</a></dt>
-<dd><p>Create all <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a> instancess from
-a list of <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances.</p>
-<p>The function also builds the <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><tt class="xref py py-class docutils literal"><span class="pre">Residue</span></tt></a>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">build_segments</code><span class="sig-paren">(</span><em>atoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#build_segments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.build_segments" title="Permalink to this definition">¶</a></dt>
+<dd><p>Create all <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></a> instancess from
+a list of <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances.</p>
+<p>The function also builds the <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Residue" title="MDAnalysis.core.AtomGroup.Residue"><code class="xref py py-class docutils literal"><span class="pre">Residue</span></code></a>
 instances by tracking residue numbers.</p>
 <p>Updating segments also changes the underlying
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances, which record
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances, which record
 to which residue and segment an atom belongs.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">structure dict, which associates a segname with a
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt></a></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">List of <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Segment" title="MDAnalysis.core.AtomGroup.Segment"><code class="xref py py-class docutils literal"><span class="pre">Segment</span></code></a>
+instances</td>
 </tr>
 </tbody>
 </table>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Now allows resids in a given <tt class="xref py py-class docutils literal"><span class="pre">Segment</span></tt> to be given in non sequential order.</p>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Now allows resids in a given <code class="xref py py-class docutils literal"><span class="pre">Segment</span></code> to be given in non sequential order.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.11.0: </span>Returns a list instead of a dict for consistency with the outputs of
+<a class="reference internal" href="#MDAnalysis.topology.core.build_residues" title="MDAnalysis.topology.core.build_residues"><code class="xref py py-func docutils literal"><span class="pre">build_residues()</span></code></a></p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.core.get_atom_mass">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">get_atom_mass</tt><big>(</big><em>element</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#get_atom_mass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.get_atom_mass" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">get_atom_mass</code><span class="sig-paren">(</span><em>element</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#get_atom_mass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.get_atom_mass" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return the atomic mass in u for <em>element</em>.</p>
-<p>Masses are looked up in <a class="reference internal" href="tables.html#MDAnalysis.topology.tables.masses" title="MDAnalysis.topology.tables.masses"><tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.topology.tables.masses</span></tt></a>.</p>
+<p>Masses are looked up in <a class="reference internal" href="tables.html#MDAnalysis.topology.tables.masses" title="MDAnalysis.topology.tables.masses"><code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.topology.tables.masses</span></code></a>.</p>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
 <p class="last">Unknown masses are set to 0.00</p>
@@ -160,15 +167,28 @@ <h1>4.20. Common functions for topology building &#8212; <a class="reference int
 
 <dl class="function">
 <dt id="MDAnalysis.topology.core.get_parser_for">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">get_parser_for</tt><big>(</big><em>filename</em>, <em>permissive=False</em>, <em>tformat=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#get_parser_for"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.get_parser_for" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">get_parser_for</code><span class="sig-paren">(</span><em>filename</em>, <em>permissive=False</em>, <em>format=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#get_parser_for"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.get_parser_for" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return the appropriate topology parser for <em>filename</em>.</p>
 <p>Automatic detection is disabled when an explicit <em>format</em> is
 provided.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><dl class="first last docutils">
+<dt><em>ValueError</em></dt>
+<dd><p class="first last">If no appropriate parser could be found.</p>
+</dd>
+</dl>
+</td>
+</tr>
+</tbody>
+</table>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.core.guess_angles">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">guess_angles</tt><big>(</big><em>bonds</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_angles"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_angles" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">guess_angles</code><span class="sig-paren">(</span><em>bonds</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_angles"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_angles" title="Permalink to this definition">¶</a></dt>
 <dd><p>Given a list of Bonds, find all angles that exist between atoms.</p>
 <p>Works by assuming that if atoms 1 &amp; 2 are bonded, and 2 &amp; 3 are bonded,
 then (1,2,3) must be an angle.</p>
@@ -176,20 +196,20 @@ <h1>4.20. Common functions for topology building &#8212; <a class="reference int
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">List of tuples defining the angles.
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">List of tuples defining the angles.
 Suitable for use in u._topology</td>
 </tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.topology.core.guess_bonds" title="MDAnalysis.topology.core.guess_bonds"><tt class="xref py py-meth docutils literal"><span class="pre">guess_bonds()</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.topology.core.guess_bonds" title="MDAnalysis.topology.core.guess_bonds"><code class="xref py py-meth docutils literal"><span class="pre">guess_bonds()</span></code></a></p>
 </div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.core.guess_atom_charge">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">guess_atom_charge</tt><big>(</big><em>atomname</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_atom_charge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_atom_charge" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">guess_atom_charge</code><span class="sig-paren">(</span><em>atomname</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_atom_charge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_atom_charge" title="Permalink to this definition">¶</a></dt>
 <dd><p>Guess atom charge from the name.</p>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
@@ -199,24 +219,24 @@ <h1>4.20. Common functions for topology building &#8212; <a class="reference int
 
 <dl class="function">
 <dt id="MDAnalysis.topology.core.guess_atom_element">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">guess_atom_element</tt><big>(</big><em>atomname</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_atom_element"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_atom_element" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">guess_atom_element</code><span class="sig-paren">(</span><em>atomname</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_atom_element"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_atom_element" title="Permalink to this definition">¶</a></dt>
 <dd><p>Guess the element of the atom from the name.</p>
 <p>Looks in dict to see if element is found, otherwise it uses the first
 character in the atomname. The table comes from CHARMM and AMBER atom
 types, where the first character is not sufficient to determine the atom
 type. Some GROMOS ions have also been added.</p>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_type" title="MDAnalysis.topology.core.guess_atom_type"><tt class="xref py py-func docutils literal"><span class="pre">guess_atom_type()</span></tt></a> and
-<a class="reference internal" href="tables.html#module-MDAnalysis.topology.tables" title="MDAnalysis.topology.tables"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tables</span></tt></a> (where the data are stored)</p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_type" title="MDAnalysis.topology.core.guess_atom_type"><code class="xref py py-func docutils literal"><span class="pre">guess_atom_type()</span></code></a> and
+<a class="reference internal" href="tables.html#module-MDAnalysis.topology.tables" title="MDAnalysis.topology.tables"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tables</span></code></a> (where the data are stored)</p>
 </div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.core.guess_atom_mass">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">guess_atom_mass</tt><big>(</big><em>atomname</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_atom_mass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_atom_mass" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">guess_atom_mass</code><span class="sig-paren">(</span><em>atomname</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_atom_mass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_atom_mass" title="Permalink to this definition">¶</a></dt>
 <dd><p>Guess a mass based on the atom name.</p>
-<p><a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_element" title="MDAnalysis.topology.core.guess_atom_element"><tt class="xref py py-func docutils literal"><span class="pre">guess_atom_element()</span></tt></a> is used to determine the kind of atom.</p>
+<p><a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_element" title="MDAnalysis.topology.core.guess_atom_element"><code class="xref py py-func docutils literal"><span class="pre">guess_atom_element()</span></code></a> is used to determine the kind of atom.</p>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
 <p class="last">Anything not recognized is simply set to 0; if you rely on the
@@ -226,20 +246,20 @@ <h1>4.20. Common functions for topology building &#8212; <a class="reference int
 
 <dl class="function">
 <dt id="MDAnalysis.topology.core.guess_atom_type">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">guess_atom_type</tt><big>(</big><em>atomname</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_atom_type"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_atom_type" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">guess_atom_type</code><span class="sig-paren">(</span><em>atomname</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_atom_type"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_atom_type" title="Permalink to this definition">¶</a></dt>
 <dd><p>Guess atom type from the name.</p>
 <p>At the moment, this function simply returns the element, as
-guessed by <a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_element" title="MDAnalysis.topology.core.guess_atom_element"><tt class="xref py py-func docutils literal"><span class="pre">guess_atom_element()</span></tt></a>.</p>
-<div class="admonition-see-also admonition seealso">
+guessed by <a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_element" title="MDAnalysis.topology.core.guess_atom_element"><code class="xref py py-func docutils literal"><span class="pre">guess_atom_element()</span></code></a>.</p>
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_element" title="MDAnalysis.topology.core.guess_atom_element"><tt class="xref py py-func docutils literal"><span class="pre">guess_atom_element()</span></tt></a> and
-<a class="reference internal" href="tables.html#module-MDAnalysis.topology.tables" title="MDAnalysis.topology.tables"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tables</span></tt></a></p>
+<p class="last"><a class="reference internal" href="#MDAnalysis.topology.core.guess_atom_element" title="MDAnalysis.topology.core.guess_atom_element"><code class="xref py py-func docutils literal"><span class="pre">guess_atom_element()</span></code></a> and
+<a class="reference internal" href="tables.html#module-MDAnalysis.topology.tables" title="MDAnalysis.topology.tables"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tables</span></code></a></p>
 </div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.core.guess_bonds">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">guess_bonds</tt><big>(</big><em>atoms</em>, <em>coords</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_bonds" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">guess_bonds</code><span class="sig-paren">(</span><em>atoms</em>, <em>coords</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_bonds" title="Permalink to this definition">¶</a></dt>
 <dd><p>Guess if bonds exist between two atoms based on their distance.</p>
 <p>Bond between two atoms is created, if the two atoms are within</p>
 <div class="math">
@@ -251,7 +271,7 @@ <h1>4.20. Common functions for topology building &#8212; <a class="reference int
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Keywords :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Keywords:</th><td class="field-body"><dl class="first docutils">
 <dt><em>fudge_factor</em></dt>
 <dd><p class="first last">The factor by which atoms must overlap eachother to be considered a
 bond.  Larger values will increase the number of bonds found. [0.72]</p>
@@ -259,9 +279,9 @@ <h1>4.20. Common functions for topology building &#8212; <a class="reference int
 <dt><em>vdwradii</em></dt>
 <dd><p class="first last">To supply custom vdwradii for atoms in the algorithm. Must be a dict
 of format {type:radii}. The default table of van der Waals radii is
-hard-coded as <tt class="xref py py-data docutils literal"><span class="pre">MDAnalysis.topology.tables.vdwradii</span></tt>.  Any user
+hard-coded as <code class="xref py py-data docutils literal"><span class="pre">MDAnalysis.topology.tables.vdwradii</span></code>.  Any user
 defined vdwradii passed as an argument will supercede the table
-values. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+values. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 <dt><em>lower_bound</em></dt>
 <dd><p class="first last">The minimum bond length. All bonds found shorter than this length will
@@ -272,12 +292,12 @@ <h1>4.20. Common functions for topology building &#8212; <a class="reference int
 <dt><em>box</em></dt>
 <dd><p class="first last">Bonds are found using a distance search, if unit cell information is
 given, periodic boundary conditions will be considered in the distance
-search. [<tt class="docutils literal"><span class="pre">None</span></tt>]</p>
+search. [<code class="docutils literal"><span class="pre">None</span></code>]</p>
 </dd>
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">List of tuples suitable for use in Universe topology building.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">List of tuples suitable for use in Universe topology building.</p>
 </td>
 </tr>
 </tbody>
@@ -291,22 +311,24 @@ <h1>4.20. Common functions for topology building &#8212; <a class="reference int
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body">ValueError if inputs are malformed or <em>vdwradii</em> data is missing.</td>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body">ValueError if inputs are malformed or <em>vdwradii</em> data is missing.</td>
 </tr>
 </tbody>
 </table>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.7.7.</span></p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Updated method internally to use more <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.9)"><tt class="xref py py-mod docutils literal"><span class="pre">numpy</span></tt></a>, should work
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.7.7.</span></p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Updated method internally to use more <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.9)"><code class="xref py py-mod docutils literal"><span class="pre">numpy</span></code></a>, should work
 faster.  Should also use less memory, previously scaled as
 <span class="math">\(O(n^2)\)</span>.  <em>vdwradii</em> argument now augments table list
 rather than replacing entirely.</p>
+</div>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.core.guess_dihedrals">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">guess_dihedrals</tt><big>(</big><em>angles</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_dihedrals"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_dihedrals" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">guess_dihedrals</code><span class="sig-paren">(</span><em>angles</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_dihedrals"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_dihedrals" title="Permalink to this definition">¶</a></dt>
 <dd><p>Given a list of Angles, find all dihedrals that exist between atoms.</p>
 <p>Works by assuming that if (1,2,3) is an angle, and 3 &amp; 4 are bonded,
 then (1,2,3,4) must be a dihedral.</p>
@@ -314,26 +336,16 @@ <h1>4.20. Common functions for topology building &#8212; <a class="reference int
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">List of tuples defining the dihedrals.
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">List of tuples defining the dihedrals.
 Suitable for use in u._topology</td>
 </tr>
 </tbody>
 </table>
 </dd></dl>
 
-<dl class="function">
-<dt id="MDAnalysis.topology.core.guess_format">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">guess_format</tt><big>(</big><em>filename</em>, <em>format=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_format"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_format" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns the type of topology file <em>filename</em>.</p>
-<p>The current heuristic simply looks at the filename extension but
-more complicated probes could be implemented here or in the
-individual packages (e.g. as static methods).</p>
-<p>If <em>format</em> is supplied then it overrides the auto detection.</p>
-</dd></dl>
-
 <dl class="function">
 <dt id="MDAnalysis.topology.core.guess_improper_dihedrals">
-<tt class="descclassname">MDAnalysis.topology.core.</tt><tt class="descname">guess_improper_dihedrals</tt><big>(</big><em>angles</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_improper_dihedrals"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_improper_dihedrals" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.core.</code><code class="descname">guess_improper_dihedrals</code><span class="sig-paren">(</span><em>angles</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/core.html#guess_improper_dihedrals"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.core.guess_improper_dihedrals" title="Permalink to this definition">¶</a></dt>
 <dd><p>Given a list of Angles, find all improper dihedrals that exist between
 atoms.</p>
 <p>Works by assuming that if (1,2,3) is an angle, and 2 &amp; 4 are bonded,
@@ -344,7 +356,7 @@ <h1>4.20. Common functions for topology building &#8212; <a class="reference int
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">List of tuples defining the improper dihedrals.
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">List of tuples defining the improper dihedrals.
 Suitable for use in u._topology</td>
 </tr>
 </tbody>
@@ -359,7 +371,7 @@ <h1>4.20. Common functions for topology building &#8212; <a class="reference int
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -374,11 +386,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="base.html" title="4.19. Base topology reader classes — MDAnalysis.topology.base"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -388,7 +400,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/init.html b/package/doc/html/documentation_pages/topology/init.html
index d5eff164d6b..19246bc4d93 100644
--- a/package/doc/html/documentation_pages/topology/init.html
+++ b/package/doc/html/documentation_pages/topology/init.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.1. Topology readers — MDAnalysis.topology &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.1. Topology readers — MDAnalysis.topology &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.2. PSF topology parser" href="PSFParser.html" />
     <link rel="prev" title="4. Topology modules" href="../topology_modules.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,18 +49,18 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../topology_modules.html" title="4. Topology modules"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">4.1. Topology readers &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.topology</span></tt></a><ul>
+<li><a class="reference internal" href="#">4.1. Topology readers &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology</span></code></a><ul>
 <li><a class="reference internal" href="#developer-notes">4.1.1. Developer Notes</a><ul>
 <li><a class="reference internal" href="#atoms">4.1.1.1. atoms</a></li>
 <li><a class="reference internal" href="#bonds">4.1.1.2. bonds</a></li>
@@ -82,12 +80,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="PSFParser.html"
                         title="next chapter">4.2. PSF topology parser</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/init.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/topology/init.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -106,10 +106,10 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.topology.__init__"></span><div class="section" id="topology-readers-mdanalysis-topology">
-<h1>4.1. Topology readers &#8212; <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology</span></tt><a class="headerlink" href="#topology-readers-mdanalysis-topology" title="Permalink to this headline">¶</a></h1>
+<h1>4.1. Topology readers &#8212; <code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology</span></code><a class="headerlink" href="#topology-readers-mdanalysis-topology" title="Permalink to this headline">¶</a></h1>
 <p>This submodule contains the topology readers. A topology file supplies the list
 of atoms in the system, their connectivity and possibly additional information
 such as B-factors, partial charges, etc. The details depend on the file format
@@ -117,8 +117,8 @@ <h1>4.1. Topology readers &#8212; <tt class="xref py py-mod docutils literal"><s
 minimum, a topology file has to contain the names of atoms in the order of the
 coordinate file and their residue names and numbers.</p>
 <p>The following table lists the currently supported topology formats.</p>
-<table border="1" class="docutils" id="supported-topology-formats">
-<caption>Table of Supported Topology Formats</caption>
+<table border="1" class="docutils" id="id15">
+<span id="supported-topology-formats"></span><caption><span class="caption-text">Table of Supported Topology Formats</span><a class="headerlink" href="#id15" title="Permalink to this table">¶</a></caption>
 <colgroup>
 <col width="19%" />
 <col width="11%" />
@@ -135,110 +135,110 @@ <h1>4.1. Topology readers &#8212; <tt class="xref py py-mod docutils literal"><s
 <td>psf</td>
 <td>reads either format, atoms, bonds, angles,
 torsions/dihedrals information is all used;
-<a class="reference internal" href="PSFParser.html#module-MDAnalysis.topology.PSFParser" title="MDAnalysis.topology.PSFParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PSFParser</span></tt></a></td>
+<a class="reference internal" href="PSFParser.html#module-MDAnalysis.topology.PSFParser" title="MDAnalysis.topology.PSFParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PSFParser</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>CHARMM CARD <a class="footnote-reference" href="#a" id="id1">[1]</a></td>
 <td>crd</td>
 <td>&#8220;CARD&#8221; coordinate output from CHARMM; deals with
 either standard or EXTended format;
-<a class="reference internal" href="CRDParser.html#module-MDAnalysis.topology.CRDParser" title="MDAnalysis.topology.CRDParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.CRDParser</span></tt></a></td>
+<a class="reference internal" href="CRDParser.html#module-MDAnalysis.topology.CRDParser" title="MDAnalysis.topology.CRDParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.CRDParser</span></code></a></td>
 </tr>
 <tr class="row-even"><td>Brookhaven <a class="footnote-reference" href="#a" id="id2">[1]</a></td>
 <td>pdb</td>
 <td>a simplified PDB format (as used in MD simulations)
 is read by default; the full format can be read by
 supplying the <cite>permissive=False</cite> flag to
-<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt>;
-<a class="reference internal" href="PrimitivePDBParser.html#module-MDAnalysis.topology.PrimitivePDBParser" title="MDAnalysis.topology.PrimitivePDBParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PrimitivePDBParser</span></tt></a> and
-<a class="reference internal" href="PDBParser.html#module-MDAnalysis.topology.PDBParser" title="MDAnalysis.topology.PDBParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PDBParser</span></tt></a></td>
+<code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code>;
+<a class="reference internal" href="PrimitivePDBParser.html#module-MDAnalysis.topology.PrimitivePDBParser" title="MDAnalysis.topology.PrimitivePDBParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PrimitivePDBParser</span></code></a> and
+<a class="reference internal" href="PDBParser.html#module-MDAnalysis.topology.PDBParser" title="MDAnalysis.topology.PDBParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PDBParser</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>XPDB <a class="footnote-reference" href="#a" id="id3">[1]</a></td>
 <td>pdb</td>
 <td>Extended PDB format (can use 5-digit residue
 numbers). To use, specify the format &#8220;XPBD&#8221;
 explicitly:
-<tt class="docutils literal"><span class="pre">Universe(...,</span> <span class="pre">topology_format=&quot;XPDB&quot;)</span></tt>.
-Module <a class="reference internal" href="../coordinates/PDB.html#module-MDAnalysis.coordinates.PDB" title="MDAnalysis.coordinates.PDB"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></tt></a></td>
+<code class="docutils literal"><span class="pre">Universe(...,</span> <span class="pre">topology_format=&quot;XPDB&quot;)</span></code>.
+Module <a class="reference internal" href="../coordinates/PDB.html#module-MDAnalysis.coordinates.PDB" title="MDAnalysis.coordinates.PDB"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></code></a></td>
 </tr>
 <tr class="row-even"><td>PQR <a class="footnote-reference" href="#a" id="id4">[1]</a></td>
 <td>pqr</td>
 <td>PDB-like but whitespace-separated files with charge
 and radius information;
-<a class="reference internal" href="PQRParser.html#module-MDAnalysis.topology.PQRParser" title="MDAnalysis.topology.PQRParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PQRParser</span></tt></a></td>
+<a class="reference internal" href="PQRParser.html#module-MDAnalysis.topology.PQRParser" title="MDAnalysis.topology.PQRParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PQRParser</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>PDBQT <a class="footnote-reference" href="#a" id="id5">[1]</a></td>
 <td>pdbqt</td>
 <td>file format used by AutoDock with atom types <em>t</em>
 and partial charges <em>q</em>. Module:
-<a class="reference internal" href="PDBQTParser.html#module-MDAnalysis.topology.PDBQTParser" title="MDAnalysis.topology.PDBQTParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PDBQTParser</span></tt></a></td>
+<a class="reference internal" href="PDBQTParser.html#module-MDAnalysis.topology.PDBQTParser" title="MDAnalysis.topology.PDBQTParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.PDBQTParser</span></code></a></td>
 </tr>
 <tr class="row-even"><td>GROMOS96 <a class="footnote-reference" href="#a" id="id6">[1]</a></td>
 <td>gro</td>
 <td>GROMOS96 coordinate file;
-<a class="reference internal" href="GROParser.html#module-MDAnalysis.topology.GROParser" title="MDAnalysis.topology.GROParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.GROParser</span></tt></a></td>
+<a class="reference internal" href="GROParser.html#module-MDAnalysis.topology.GROParser" title="MDAnalysis.topology.GROParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.GROParser</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>AMBER</td>
 <td>top,
 prmtop</td>
 <td>simple AMBER format reader (only supports a subset
 of flags);
-<a class="reference internal" href="TOPParser.html#module-MDAnalysis.topology.TOPParser" title="MDAnalysis.topology.TOPParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.TOPParser</span></tt></a></td>
+<a class="reference internal" href="TOPParser.html#module-MDAnalysis.topology.TOPParser" title="MDAnalysis.topology.TOPParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.TOPParser</span></code></a></td>
 </tr>
 <tr class="row-even"><td>DESRES <a class="footnote-reference" href="#a" id="id7">[1]</a></td>
 <td>dms</td>
 <td>DESRES molecular sturcture reader (only supports
 the atom and bond records);
-<a class="reference internal" href="DMSParser.html#module-MDAnalysis.topology.DMSParser" title="MDAnalysis.topology.DMSParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.DMSParser</span></tt></a></td>
+<a class="reference internal" href="DMSParser.html#module-MDAnalysis.topology.DMSParser" title="MDAnalysis.topology.DMSParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.DMSParser</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>TPR <a class="footnote-reference" href="#b" id="id8">[2]</a></td>
 <td>tpr</td>
 <td>Gromacs portable run input reader (limited
 experimental support for some of the more recent
 versions of the file format);
-<a class="reference internal" href="TPRParser.html#module-MDAnalysis.topology.TPRParser" title="MDAnalysis.topology.TPRParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.TPRParser</span></tt></a></td>
+<a class="reference internal" href="TPRParser.html#module-MDAnalysis.topology.TPRParser" title="MDAnalysis.topology.TPRParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.TPRParser</span></code></a></td>
 </tr>
 <tr class="row-even"><td>MOL2 <a class="footnote-reference" href="#a" id="id9">[1]</a></td>
 <td>mol2</td>
 <td>Tripos MOL2 molecular structure format;
-<a class="reference internal" href="MOL2Parser.html#module-MDAnalysis.topology.MOL2Parser" title="MDAnalysis.topology.MOL2Parser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.MOL2Parser</span></tt></a></td>
+<a class="reference internal" href="MOL2Parser.html#module-MDAnalysis.topology.MOL2Parser" title="MDAnalysis.topology.MOL2Parser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.MOL2Parser</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>LAMMPS <a class="footnote-reference" href="#a" id="id10">[1]</a></td>
 <td>data</td>
 <td>LAMMPS Data file parser
-<a class="reference internal" href="LAMMPSParser.html#module-MDAnalysis.topology.LAMMPSParser" title="MDAnalysis.topology.LAMMPSParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.LAMMPSParser</span></tt></a></td>
+<a class="reference internal" href="LAMMPSParser.html#module-MDAnalysis.topology.LAMMPSParser" title="MDAnalysis.topology.LAMMPSParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.LAMMPSParser</span></code></a></td>
 </tr>
 <tr class="row-even"><td>XYZ <a class="footnote-reference" href="#a" id="id11">[1]</a></td>
 <td>xyz</td>
 <td>XYZ File Parser.  Reads only the labels from atoms and
 constructs minimal topology data.
-<a class="reference internal" href="XYZParser.html#module-MDAnalysis.topology.XYZParser" title="MDAnalysis.topology.XYZParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.XYZParser</span></tt></a></td>
+<a class="reference internal" href="XYZParser.html#module-MDAnalysis.topology.XYZParser" title="MDAnalysis.topology.XYZParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.XYZParser</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>GAMESS <a class="footnote-reference" href="#a" id="id12">[1]</a></td>
 <td>gms,
 log</td>
 <td>GAMESS output parser. Read only atoms of assembly
 section (atom, elems and coords) and construct topology.
-<a class="reference internal" href="GMSParser.html#module-MDAnalysis.topology.GMSParser" title="MDAnalysis.topology.GMSParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.GMSParser</span></tt></a></td>
+<a class="reference internal" href="GMSParser.html#module-MDAnalysis.topology.GMSParser" title="MDAnalysis.topology.GMSParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.GMSParser</span></code></a></td>
 </tr>
 <tr class="row-even"><td>DL_Poly <a class="footnote-reference" href="#a" id="id13">[1]</a></td>
 <td>config</td>
 <td>DL_Poly CONFIG file.  Reads only the atom names.
 If atoms are written out of order, will correct the
 order.
-<a class="reference internal" href="DLPolyParser.html#module-MDAnalysis.topology.DLPolyParser" title="MDAnalysis.topology.DLPolyParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></tt></a></td>
+<a class="reference internal" href="DLPolyParser.html#module-MDAnalysis.topology.DLPolyParser" title="MDAnalysis.topology.DLPolyParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></code></a></td>
 </tr>
 <tr class="row-odd"><td>DL_Poly <a class="footnote-reference" href="#a" id="id14">[1]</a></td>
 <td>history</td>
 <td>DL_Poly HISTORY file.  Reads only the atom names.
 If atoms are written out of order, will correct the
 order.
-<a class="reference internal" href="DLPolyParser.html#module-MDAnalysis.topology.DLPolyParser" title="MDAnalysis.topology.DLPolyParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></tt></a></td>
+<a class="reference internal" href="DLPolyParser.html#module-MDAnalysis.topology.DLPolyParser" title="MDAnalysis.topology.DLPolyParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></code></a></td>
 </tr>
 <tr class="row-even"><td>Hoomd XML</td>
 <td>xml</td>
 <td><a class="reference external" href="http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html">HOOMD XML</a> topology file.  Reads atom types, masses, and
 charges if possible. Also reads bonds, angles, and dihedrals.
-<a class="reference internal" href="HoomdXMLParser.html#module-MDAnalysis.topology.HoomdXMLParser" title="MDAnalysis.topology.HoomdXMLParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.HoomdXMLParser</span></tt></a></td>
+<a class="reference internal" href="HoomdXMLParser.html#module-MDAnalysis.topology.HoomdXMLParser" title="MDAnalysis.topology.HoomdXMLParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.HoomdXMLParser</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -247,10 +247,10 @@ <h1>4.1. Topology readers &#8212; <tt class="xref py py-mod docutils literal"><s
 <tbody valign="top">
 <tr><td class="label">[1]</td><td><em>(<a class="fn-backref" href="#id1">1</a>, <a class="fn-backref" href="#id2">2</a>, <a class="fn-backref" href="#id3">3</a>, <a class="fn-backref" href="#id4">4</a>, <a class="fn-backref" href="#id5">5</a>, <a class="fn-backref" href="#id6">6</a>, <a class="fn-backref" href="#id7">7</a>, <a class="fn-backref" href="#id9">8</a>, <a class="fn-backref" href="#id10">9</a>, <a class="fn-backref" href="#id11">10</a>, <a class="fn-backref" href="#id12">11</a>, <a class="fn-backref" href="#id13">12</a>, <a class="fn-backref" href="#id14">13</a>)</em> This format can also be used to provide <em>coordinates</em> so that
 it is possible to create a full
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-mod docutils literal"><span class="pre">Universe</span></tt></a> by simply providing a
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-mod docutils literal"><span class="pre">Universe</span></code></a> by simply providing a
 file of this format as the sole argument to
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-mod docutils literal"><span class="pre">Universe</span></tt></a>: <tt class="docutils literal"><span class="pre">u</span> <span class="pre">=</span>
-<span class="pre">Universe(filename)</span></tt></td></tr>
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-mod docutils literal"><span class="pre">Universe</span></code></a>: <code class="docutils literal"><span class="pre">u</span> <span class="pre">=</span>
+<span class="pre">Universe(filename)</span></code></td></tr>
 </tbody>
 </table>
 <table class="docutils footnote" frame="void" id="b" rules="none">
@@ -258,24 +258,25 @@ <h1>4.1. Topology readers &#8212; <tt class="xref py py-mod docutils literal"><s
 <tbody valign="top">
 <tr><td class="label"><a class="fn-backref" href="#id8">[2]</a></td><td>The Gromacs TPR format contains coordinate information but
 parsing coordinates from a TPR file is currently not implemented
-in <a class="reference internal" href="TPRParser.html#module-MDAnalysis.topology.TPRParser" title="MDAnalysis.topology.TPRParser"><tt class="xref py py-mod docutils literal"><span class="pre">TPRParser</span></tt></a>.</td></tr>
+in <a class="reference internal" href="TPRParser.html#module-MDAnalysis.topology.TPRParser" title="MDAnalysis.topology.TPRParser"><code class="xref py py-mod docutils literal"><span class="pre">TPRParser</span></code></a>.</td></tr>
 </tbody>
 </table>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="../coordinates_modules.html#coordinates"><em>Coordinates modules</em></a> with the <a class="reference internal" href="../coordinates/init.html#id1"><em>Table of supported coordinate formats</em></a></p>
+<p class="last"><a class="reference internal" href="../coordinates_modules.html#coordinates"><span>Coordinates modules</span></a> with the <a class="reference internal" href="../coordinates/init.html#id1"><span>Table of supported coordinate formats</span></a></p>
 </div>
 <div class="section" id="developer-notes">
 <h2>4.1.1. Developer Notes<a class="headerlink" href="#developer-notes" title="Permalink to this headline">¶</a></h2>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.8.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.8.</span></p>
+</div>
 <p>Topology information consists of data that do not change over time,
 i.e. information that is the same for all time steps of a
 trajectory. This includes</p>
 <ul class="simple">
 <li>identity of atoms (name, type, number, partial charge, ...) and to
 which residue and segment they belong; atoms are identified in
-MDAnalysis by their <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.index" title="MDAnalysis.core.AtomGroup.Atom.index"><tt class="xref py py-attr docutils literal"><span class="pre">index</span></tt></a>,
+MDAnalysis by their <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.index" title="MDAnalysis.core.AtomGroup.Atom.index"><code class="xref py py-attr docutils literal"><span class="pre">index</span></code></a>,
 an integer number starting at 0 and incremented in the order of
 atoms found in the topology.</li>
 <li>bonds (pairs of atoms)</li>
@@ -287,11 +288,11 @@ <h2>4.1.1. Developer Notes<a class="headerlink" href="#developer-notes" title="P
 basic, the topology is simply a list of atoms to be associated with a
 list of coordinates.</p>
 <p>The current implementation contains submodules for different topology
-file types. Each submodule <em>must</em> contain a function <tt class="xref py py-func docutils literal"><span class="pre">parse()</span></tt>:</p>
+file types. Each submodule <em>must</em> contain a function <code class="xref py py-func docutils literal"><span class="pre">parse()</span></code>:</p>
 <p>The function returns the basic MDAnalysis representation of the
 topology. At the moment, this is simply a dictionary with keys
 <em>atoms</em>, <em>bonds</em>, <em>angles</em>, <em>dihedrals</em>, <em>impropers</em>. The dictionary is
-stored as <tt class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.AtomGroup.Universe._topology</span></tt>.</p>
+stored as <code class="xref py py-attr docutils literal"><span class="pre">MDAnalysis.AtomGroup.Universe._topology</span></code>.</p>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
 <p class="last">The internal dictionary representation is subject to change. User
@@ -299,26 +300,26 @@ <h2>4.1.1. Developer Notes<a class="headerlink" href="#developer-notes" title="P
 provided here is solely for developers who need to work with the
 existing parsers.</p>
 </div>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <p class="last"><a class="reference external" href="https://github.com/MDAnalysis/mdanalysis/wiki/TopologyDataStructures">Topology Data Structures Wiki page</a></p>
 </div>
 <p>The format of the individual keys is the following (see
-<tt class="xref py py-mod docutils literal"><span class="pre">PSFParser</span></tt> for a reference implementation):</p>
+<code class="xref py py-mod docutils literal"><span class="pre">PSFParser</span></code> for a reference implementation):</p>
 <div class="section" id="atoms">
 <h3>4.1.1.1. atoms<a class="headerlink" href="#atoms" title="Permalink to this headline">¶</a></h3>
-<p>The <strong>atoms</strong> are represented as a <a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a> of
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> instances. The parser needs
-to initialize the <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><tt class="xref py py-class docutils literal"><span class="pre">Atom</span></tt></a> objects
+<p>The <strong>atoms</strong> are represented as a <a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> instances. The parser needs
+to initialize the <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom" title="MDAnalysis.core.AtomGroup.Atom"><code class="xref py py-class docutils literal"><span class="pre">Atom</span></code></a> objects
 with the data read from the topology file.</p>
 <p>The order of atoms in the list must correspond to the sequence of
 atoms in the topology file. The atom&#8217;s
-<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.index" title="MDAnalysis.core.AtomGroup.Atom.index"><tt class="xref py py-attr docutils literal"><span class="pre">index</span></tt></a> corresponds to its
+<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.index" title="MDAnalysis.core.AtomGroup.Atom.index"><code class="xref py py-attr docutils literal"><span class="pre">index</span></code></a> corresponds to its
 index in this list.</p>
 </div>
 <div class="section" id="bonds">
 <h3>4.1.1.2. bonds<a class="headerlink" href="#bonds" title="Permalink to this headline">¶</a></h3>
-<p><strong>Bonds</strong> are represented as a <tt class="xref py py-class docutils literal"><span class="pre">tuple</span></tt> of <tt class="xref py py-class docutils literal"><span class="pre">tuple</span></tt>. Each tuple
+<p><strong>Bonds</strong> are represented as a <code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> of <code class="xref py py-class docutils literal"><span class="pre">tuple</span></code>. Each tuple
 contains two atom numbers, which indicate the atoms between which the
 bond is formed. Only one of the two permutations is stored, typically
 the one with the lower atom number first.</p>
@@ -331,20 +332,20 @@ <h3>4.1.1.3. bondorder<a class="headerlink" href="#bondorder" title="Permalink t
 </div>
 <div class="section" id="angles">
 <h3>4.1.1.4. angles<a class="headerlink" href="#angles" title="Permalink to this headline">¶</a></h3>
-<p><strong>Angles</strong> are represented by a <a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a> of <tt class="xref py py-class docutils literal"><span class="pre">tuple</span></tt>. Each
+<p><strong>Angles</strong> are represented by a <a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <code class="xref py py-class docutils literal"><span class="pre">tuple</span></code>. Each
 tuple contains three atom numbers.  The second of these numbers
 represents the apex of the angle.</p>
 </div>
 <div class="section" id="dihedrals">
 <h3>4.1.1.5. dihedrals<a class="headerlink" href="#dihedrals" title="Permalink to this headline">¶</a></h3>
-<p><strong>Proper dihedral angles</strong> are represented by a <a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a> of <tt class="xref py py-class docutils literal"><span class="pre">tuple</span></tt>. Each
+<p><strong>Proper dihedral angles</strong> are represented by a <a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <code class="xref py py-class docutils literal"><span class="pre">tuple</span></code>. Each
 tuple contains four atom numbers. The angle of the torsion
 is defined by the angle between the planes formed by atoms 1, 2, and 3,
 and 2, 3, and 4.</p>
 </div>
 <div class="section" id="impropers">
 <h3>4.1.1.6. impropers<a class="headerlink" href="#impropers" title="Permalink to this headline">¶</a></h3>
-<p><strong>Improper dihedral angles</strong> are represented by a <a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a> of <tt class="xref py py-class docutils literal"><span class="pre">tuple</span></tt>. Each
+<p><strong>Improper dihedral angles</strong> are represented by a <a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <code class="xref py py-class docutils literal"><span class="pre">tuple</span></code>. Each
 tuple contains four atom numbers.  The angle of the improper torsion
 is again defined by the angle between the planes formed by atoms 1, 2, and 3,
 and 2, 3, and 4.  Improper dihedrals differ from regular dihedrals as the
@@ -360,7 +361,7 @@ <h3>4.1.1.6. impropers<a class="headerlink" href="#impropers" title="Permalink t
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -375,11 +376,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../topology_modules.html" title="4. Topology modules"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -389,7 +390,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/tables.html b/package/doc/html/documentation_pages/topology/tables.html
index 1db232de222..606ef63d51f 100644
--- a/package/doc/html/documentation_pages/topology/tables.html
+++ b/package/doc/html/documentation_pages/topology/tables.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.21. MDAnalysis topology tables &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.21. MDAnalysis topology tables &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
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+        VERSION:     '0.11.0',
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         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
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     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="4.22. Utility functions for the TPR topology parser" href="tpr_util.html" />
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+    <div class="related" role="navigation" aria-label="related navigation">
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              accesskey="P">previous</a> |</li>
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-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
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+                        title="previous chapter">4.20. Common functions for topology building &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology.core</span></code></a></p>
   <h4>Next topic</h4>
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-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/tables.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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+  <div role="note" aria-label="source link">
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   <span class="target" id="module-MDAnalysis.topology.tables"></span><div class="section" id="mdanalysis-topology-tables">
 <h1>4.21. MDAnalysis topology tables<a class="headerlink" href="#mdanalysis-topology-tables" title="Permalink to this headline">¶</a></h1>
@@ -98,25 +98,25 @@ <h1>4.21. MDAnalysis topology tables<a class="headerlink" href="#mdanalysis-topo
 tables are dictionaries that are indexed by the element.</p>
 <dl class="data">
 <dt id="MDAnalysis.topology.tables.atomelements">
-<tt class="descclassname">MDAnalysis.topology.tables.</tt><tt class="descname">atomelements</tt><em class="property"> = {'BC': 'C', 'K+': 'K', 'AC': 'C', 'LIT': 'LI', 'CA2+': 'CA', 'FE': 'FE', 'BR': 'BR', 'CAL': 'CA', 'MG2+': 'MG', 'CL-': 'CL', 'CLAL': 'CL', 'SOD': 'NA', 'CS+': 'CS', 'NA': 'NA', 'POT': 'K', 'LI': 'LI', 'CES': 'CS', 'RB': 'RB', 'FE2': 'FE', 'IOD': 'I', 'ZN': 'ZN', 'CL': 'CL', 'K': 'K', 'CLA': 'CL', 'QR': 'RB', 'CS': 'CS', 'CU': 'CU', 'MG': 'MG', 'C0': 'CA', 'NA+': 'NA', 'LI+': 'LI', 'QC': 'CE', 'QK': 'K', 'QL': 'LI', 'QN': 'NA'}</em><a class="headerlink" href="#MDAnalysis.topology.tables.atomelements" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tables.</code><code class="descname">atomelements</code><em class="property"> = {'BC': 'C', 'K+': 'K', 'AC': 'C', 'LIT': 'LI', 'CA2+': 'CA', 'FE': 'FE', 'BR': 'BR', 'CAL': 'CA', 'MG2+': 'MG', 'CL-': 'CL', 'CLAL': 'CL', 'SOD': 'NA', 'CS+': 'CS', 'NA': 'NA', 'POT': 'K', 'LI': 'LI', 'CES': 'CS', 'RB': 'RB', 'FE2': 'FE', 'IOD': 'I', 'ZN': 'ZN', 'CL': 'CL', 'K': 'K', 'CLA': 'CL', 'QR': 'RB', 'CS': 'CS', 'CU': 'CU', 'MG': 'MG', 'C0': 'CA', 'NA+': 'NA', 'LI+': 'LI', 'QC': 'CE', 'QK': 'K', 'QL': 'LI', 'QN': 'NA'}</em><a class="headerlink" href="#MDAnalysis.topology.tables.atomelements" title="Permalink to this definition">¶</a></dt>
 <dd><p>Dictionary with hard-coded special atom names, used for guessing atom types
-with <a class="reference internal" href="core.html#MDAnalysis.topology.core.guess_atom_type" title="MDAnalysis.topology.core.guess_atom_type"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.core.guess_atom_type()</span></tt></a>.</p>
+with <a class="reference internal" href="core.html#MDAnalysis.topology.core.guess_atom_type" title="MDAnalysis.topology.core.guess_atom_type"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.core.guess_atom_type()</span></code></a>.</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.topology.tables.masses">
-<tt class="descclassname">MDAnalysis.topology.tables.</tt><tt class="descname">masses</tt><em class="property"> = {'Ru': 101.07, 'Yb': 173.04, 'Re': 186.207, 'Rf': 261.0, 'Ra': 226.025, 'BR': 79.904, 'Rn': 222.0, 'Rh': 102.9055, 'Be': 9.012182, 'Ba': 137.327, 'Bh': 262.0, 'Bi': 208.98037, 'Bk': 247.0, 'Se': 78.96, 'RB': 85.4678, 'H': 1.008, 'P': 30.974, 'Os': 190.2, 'Ge': 72.61, 'Gd': 157.25, 'Ga': 69.723, 'Pr': 140.90765, 'Pt': 195.08, 'Pu': 244.0, 'ZN': 65.37, 'Pb': 207.2, 'Pa': 231.0359, 'Pd': 106.42, 'Xe': 131.29, 'Po': 209.0, 'HE': 4.0026, 'Hs': 265.0, 'Ho': 164.93032, 'Hf': 178.49, 'Hg': 200.59, 'Md': 258.0, 'C': 12.011, 'K': 39.102, 'Mn': 54.93805, 'O': 15.999, 'Mt': 266.0, 'S': 32.06, 'W': 183.85, 'MG': 24.305, 'Eu': 151.965, 'Es': 252.0, 'Er': 167.26, 'Ni': 58.6934, 'No': 259.0, 'Na': 22.989768, 'Nb': 92.90638, 'Nd': 144.24, 'FE': 55.847, 'Np': 237.048, 'Fr': 223.0, 'NA': 22.98977, 'NE': 20.1797, 'Fm': 257.0, 'B': 10.811, 'F': 18.998, 'Sr': 87.62, 'CA': 40.08, 'N': 14.007, 'Kr': 83.8, 'Si': 28.0855, 'Sn': 118.71, 'Sm': 150.36, 'V': 50.9415, 'CS': 132.9, 'Sb': 121.757, 'Sg': 263.0, 'CU': 63.546, 'Co': 58.9332, 'Cm': 247.0, 'Cf': 251.0, 'Ce': 140.116, 'Cd': 112.411, 'Tm': 168.93421, 'Cr': 51.9961, 'La': 138.9055, 'Li': 6.941, 'Tl': 204.3833, 'Lu': 174.967, 'Lr': 262.0, 'Th': 232.0381, 'Ti': 47.88, 'Te': 127.6, 'Tb': 158.92534, 'Tc': 98.0, 'Ta': 180.9479, 'CL': 35.45, 'Db': 262.0, 'Zr': 91.224, 'Dy': 162.5, 'Pm': 145.0, 'I': 126.9045, 'U': 238.0289, 'Y': 88.90585, 'Sc': 44.95591, 'Ac': 227.028, 'Ag': 107.8682, 'Ir': 192.22, 'Am': 243.0, 'Al': 26.981539, 'As': 74.92159, 'Ar': 39.948, 'Au': 196.96654, 'At': 210.0, 'In': 114.82, 'Mo': 95.94}</em><a class="headerlink" href="#MDAnalysis.topology.tables.masses" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tables.</code><code class="descname">masses</code><em class="property"> = {'Ru': 101.07, 'Yb': 173.04, 'Re': 186.207, 'Rf': 261.0, 'Ra': 226.025, 'BR': 79.904, 'Rn': 222.0, 'Rh': 102.9055, 'Be': 9.012182, 'Ba': 137.327, 'Bh': 262.0, 'Bi': 208.98037, 'Bk': 247.0, 'Se': 78.96, 'RB': 85.4678, 'H': 1.008, 'P': 30.974, 'Os': 190.2, 'Ge': 72.61, 'Gd': 157.25, 'Ga': 69.723, 'Pr': 140.90765, 'Pt': 195.08, 'Pu': 244.0, 'ZN': 65.37, 'Pb': 207.2, 'Pa': 231.0359, 'Pd': 106.42, 'Xe': 131.29, 'Po': 209.0, 'HE': 4.0026, 'Hs': 265.0, 'Ho': 164.93032, 'Hf': 178.49, 'Hg': 200.59, 'Md': 258.0, 'C': 12.011, 'K': 39.102, 'Mn': 54.93805, 'O': 15.999, 'Mt': 266.0, 'S': 32.06, 'W': 183.85, 'MG': 24.305, 'Eu': 151.965, 'Es': 252.0, 'Er': 167.26, 'Ni': 58.6934, 'No': 259.0, 'Na': 22.989768, 'Nb': 92.90638, 'Nd': 144.24, 'FE': 55.847, 'Np': 237.048, 'Fr': 223.0, 'NA': 22.98977, 'NE': 20.1797, 'Fm': 257.0, 'B': 10.811, 'F': 18.998, 'Sr': 87.62, 'CA': 40.08, 'N': 14.007, 'Kr': 83.8, 'Si': 28.0855, 'Sn': 118.71, 'Sm': 150.36, 'V': 50.9415, 'CS': 132.9, 'Sb': 121.757, 'Sg': 263.0, 'CU': 63.546, 'Co': 58.9332, 'Cm': 247.0, 'Cf': 251.0, 'Ce': 140.116, 'Cd': 112.411, 'Tm': 168.93421, 'Cr': 51.9961, 'La': 138.9055, 'Li': 6.941, 'Tl': 204.3833, 'Lu': 174.967, 'Lr': 262.0, 'Th': 232.0381, 'Ti': 47.88, 'Te': 127.6, 'Tb': 158.92534, 'Tc': 98.0, 'Ta': 180.9479, 'CL': 35.45, 'Db': 262.0, 'Zr': 91.224, 'Dy': 162.5, 'Pm': 145.0, 'I': 126.9045, 'U': 238.0289, 'Y': 88.90585, 'Sc': 44.95591, 'Ac': 227.028, 'Ag': 107.8682, 'Ir': 192.22, 'Am': 243.0, 'Al': 26.981539, 'As': 74.92159, 'Ar': 39.948, 'Au': 196.96654, 'At': 210.0, 'In': 114.82, 'Mo': 95.94}</em><a class="headerlink" href="#MDAnalysis.topology.tables.masses" title="Permalink to this definition">¶</a></dt>
 <dd><p>Dictionary table with atomic masses in u, indexed by the element from
-<a class="reference internal" href="#MDAnalysis.topology.tables.atomelements" title="MDAnalysis.topology.tables.atomelements"><tt class="xref py py-data docutils literal"><span class="pre">atomelements</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.topology.tables.atomelements" title="MDAnalysis.topology.tables.atomelements"><code class="xref py py-data docutils literal"><span class="pre">atomelements</span></code></a>.</p>
 </dd></dl>
 
 <p>The original raw data are stored as multi-line strings that are
-translated into dictionaries with <a class="reference internal" href="#MDAnalysis.topology.tables.kv2dict" title="MDAnalysis.topology.tables.kv2dict"><tt class="xref py py-func docutils literal"><span class="pre">kv2dict()</span></tt></a>. In the future,
+translated into dictionaries with <a class="reference internal" href="#MDAnalysis.topology.tables.kv2dict" title="MDAnalysis.topology.tables.kv2dict"><code class="xref py py-func docutils literal"><span class="pre">kv2dict()</span></code></a>. In the future,
 these tables might be moved into external data files; see
-<a class="reference internal" href="#MDAnalysis.topology.tables.kv2dict" title="MDAnalysis.topology.tables.kv2dict"><tt class="xref py py-func docutils literal"><span class="pre">kv2dict()</span></tt></a> for explanation of the file format.</p>
+<a class="reference internal" href="#MDAnalysis.topology.tables.kv2dict" title="MDAnalysis.topology.tables.kv2dict"><code class="xref py py-func docutils literal"><span class="pre">kv2dict()</span></code></a> for explanation of the file format.</p>
 <dl class="function">
 <dt id="MDAnalysis.topology.tables.kv2dict">
-<tt class="descclassname">MDAnalysis.topology.tables.</tt><tt class="descname">kv2dict</tt><big>(</big><em>s</em>, <em>convertor=&lt;type 'str'&gt;</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tables.html#kv2dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tables.kv2dict" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tables.</code><code class="descname">kv2dict</code><span class="sig-paren">(</span><em>s</em>, <em>convertor=&lt;type 'str'&gt;</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tables.html#kv2dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tables.kv2dict" title="Permalink to this definition">¶</a></dt>
 <dd><p>Primitive ad-hoc parser of a key-value record list.</p>
 <ul class="simple">
 <li>The string <em>s</em> should contain each key-value pair on a separate
@@ -127,22 +127,22 @@ <h1>4.21. MDAnalysis topology tables<a class="headerlink" href="#mdanalysis-topo
 <li>Leading whitespace is ignored.</li>
 </ul>
 <p>The <em>convertor</em> is a function that converts its single argument to
-a valid Python type. The default is <tt class="xref py py-func docutils literal"><span class="pre">str()</span></tt> but other
-possibilities are <tt class="xref py py-func docutils literal"><span class="pre">int()</span></tt> (for integers) or <tt class="xref py py-func docutils literal"><span class="pre">float()</span></tt> for
+a valid Python type. The default is <code class="xref py py-func docutils literal"><span class="pre">str()</span></code> but other
+possibilities are <code class="xref py py-func docutils literal"><span class="pre">int()</span></code> (for integers) or <code class="xref py py-func docutils literal"><span class="pre">float()</span></code> for
 floating point numbers.</p>
 </dd></dl>
 
 <p>The raw tables are stored in the strings</p>
 <dl class="data">
 <dt id="MDAnalysis.topology.tables.TABLE_ATOMELEMENTS">
-<tt class="descclassname">MDAnalysis.topology.tables.</tt><tt class="descname">TABLE_ATOMELEMENTS</tt><em class="property"> = '\n# translation of atomnames to types/element\n# based on CHARMM and AMBER usage with a little bit of GROMOS (and PROPKA)\n# NOTE: CL might be ambiguous and is interpreted as chloride!\n\n# --------- ------------------\n# atomname   element\n# --------- ------------------\n\n# Bromide\nBR           BR\n\n# Calcium\nCAL          CA\nC0           CA\nCA2+         CA\n\n# Cesium\nCES          CS\n\n# Chloride\nCLA          CL\nCLAL         CL\nCL           CL\nCL-          CL\n\n# Iodide\nIOD          I\n\n# Iron\nFE           FE\nFE2          FE\n\n# Lithium\nLIT          LI\nLI           LI\nLI+          LI\nQL           LI\n\n# Magnesium\nMG           MG\nMG2+         MG\n\n# Noble gases\n## XXX collides with NE, HE in Arg  XXX\n## XXX so we remove the noble gases XXX\n##HE           HE\n##NE           NE\n\n# Potassium\nK            K\nPOT          K\nK+           K\nQK           K\n\n# Sodium\nSOD          NA\nNA           NA\nNA+          NA\nQN           NA\n\n# Zink\nZN           ZN\n\n# Copper\nCU           CU\n\n# Cesium\nCS           CS\nCS+          CS\nCES          CS\n\n# Cerium??\nQC           CE\n\n# Rubidium\nRB           RB\nQR           RB\n\n# special carbons (Amber?)\nBC           C\nAC           C\n\n# other types are guessed from the name; see\n# topology.core.guess_atom_elements()\n'</em><a class="headerlink" href="#MDAnalysis.topology.tables.TABLE_ATOMELEMENTS" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tables.</code><code class="descname">TABLE_ATOMELEMENTS</code><em class="property"> = '\n# translation of atomnames to types/element\n# based on CHARMM and AMBER usage with a little bit of GROMOS (and PROPKA)\n# NOTE: CL might be ambiguous and is interpreted as chloride!\n\n# --------- ------------------\n# atomname   element\n# --------- ------------------\n\n# Bromide\nBR           BR\n\n# Calcium\nCAL          CA\nC0           CA\nCA2+         CA\n\n# Cesium\nCES          CS\n\n# Chloride\nCLA          CL\nCLAL         CL\nCL           CL\nCL-          CL\n\n# Iodide\nIOD          I\n\n# Iron\nFE           FE\nFE2          FE\n\n# Lithium\nLIT          LI\nLI           LI\nLI+          LI\nQL           LI\n\n# Magnesium\nMG           MG\nMG2+         MG\n\n# Noble gases\n## XXX collides with NE, HE in Arg  XXX\n## XXX so we remove the noble gases XXX\n##HE           HE\n##NE           NE\n\n# Potassium\nK            K\nPOT          K\nK+           K\nQK           K\n\n# Sodium\nSOD          NA\nNA           NA\nNA+          NA\nQN           NA\n\n# Zink\nZN           ZN\n\n# Copper\nCU           CU\n\n# Cesium\nCS           CS\nCS+          CS\nCES          CS\n\n# Cerium??\nQC           CE\n\n# Rubidium\nRB           RB\nQR           RB\n\n# special carbons (Amber?)\nBC           C\nAC           C\n\n# other types are guessed from the name; see\n# topology.core.guess_atom_elements()\n'</em><a class="headerlink" href="#MDAnalysis.topology.tables.TABLE_ATOMELEMENTS" title="Permalink to this definition">¶</a></dt>
 <dd><p>Table with hard-coded special atom names, used for guessing atom types
-with <a class="reference internal" href="core.html#MDAnalysis.topology.core.guess_atom_element" title="MDAnalysis.topology.core.guess_atom_element"><tt class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.core.guess_atom_element()</span></tt></a>.</p>
+with <a class="reference internal" href="core.html#MDAnalysis.topology.core.guess_atom_element" title="MDAnalysis.topology.core.guess_atom_element"><code class="xref py py-func docutils literal"><span class="pre">MDAnalysis.topology.core.guess_atom_element()</span></code></a>.</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.topology.tables.TABLE_MASSES">
-<tt class="descclassname">MDAnalysis.topology.tables.</tt><tt class="descname">TABLE_MASSES</tt><em class="property"> = '\n# masses for elements in atomic units (u)\n# (taken from CHARMM and Gromacs atommass.dat)\n\n#------------ -----------\n# atomtype    mass\n#------------ -----------\nAc    227.028\nAl    26.981539\nAm    243\nSb    121.757\nAr    39.948\nAs    74.92159\nAt    210\nBa    137.327\nBk    247\nBe    9.012182\nBi    208.98037\nBh    262\nB     10.811\nBR    79.90400\nCd    112.411\nCA    40.08000\nCf    251\nC     12.01100\nCe    140.11600\nCS    132.90000\nCL    35.45000\nCr    51.9961\nCo    58.9332\nCU    63.54600\nCm    247\nDb    262\nDy    162.5\nEs    252\nEr    167.26\nEu    151.965\nFm    257\nF     18.99800\nFr    223\nGd    157.25\nGa    69.723\nGe    72.61\nAu    196.96654\nHf    178.49\nHs    265\nHE    4.00260\nHo    164.93032\nH     1.00800\nIn    114.82\nI     126.90450\nIr    192.22\nFE    55.84700\nKr    83.8\nLa    138.9055\nLr    262\nPb    207.2\nLi    6.941\nLu    174.967\nMG    24.30500\nMn    54.93805\nMt    266\nMd    258\nHg    200.59\nMo    95.94\nN     14.00700\nNA    22.98977\nNd    144.24\nNE    20.17970\nNp    237.048\nNi    58.6934\nNb    92.90638\nNo    259\nOs    190.2\nO     15.99900\nPd    106.42\nP     30.97400\nPt    195.08\nPu    244\nPo    209\nK     39.10200\nPr    140.90765\nPm    145\nPa    231.0359\nRa    226.025\nRn    222\nRe    186.207\nRh    102.9055\nRB    85.46780\nRu    101.07\nRf    261\nSm    150.36\nSc    44.95591\nSg    263\nSe    78.96\nSi    28.0855\nAg    107.8682\nNa    22.989768\nSr    87.62\nS     32.06000\nTa    180.9479\nTc    98\nTe    127.6\nTb    158.92534\nTl    204.3833\nTh    232.0381\nTm    168.93421\nSn    118.71\nTi    47.88\nW     183.85\nU     238.0289\nV     50.9415\nXe    131.29\nYb    173.04\nY     88.90585\nZN    65.37000\nZr    91.224\n'</em><a class="headerlink" href="#MDAnalysis.topology.tables.TABLE_MASSES" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tables.</code><code class="descname">TABLE_MASSES</code><em class="property"> = '\n# masses for elements in atomic units (u)\n# (taken from CHARMM and Gromacs atommass.dat)\n\n#------------ -----------\n# atomtype    mass\n#------------ -----------\nAc    227.028\nAl    26.981539\nAm    243\nSb    121.757\nAr    39.948\nAs    74.92159\nAt    210\nBa    137.327\nBk    247\nBe    9.012182\nBi    208.98037\nBh    262\nB     10.811\nBR    79.90400\nCd    112.411\nCA    40.08000\nCf    251\nC     12.01100\nCe    140.11600\nCS    132.90000\nCL    35.45000\nCr    51.9961\nCo    58.9332\nCU    63.54600\nCm    247\nDb    262\nDy    162.5\nEs    252\nEr    167.26\nEu    151.965\nFm    257\nF     18.99800\nFr    223\nGd    157.25\nGa    69.723\nGe    72.61\nAu    196.96654\nHf    178.49\nHs    265\nHE    4.00260\nHo    164.93032\nH     1.00800\nIn    114.82\nI     126.90450\nIr    192.22\nFE    55.84700\nKr    83.8\nLa    138.9055\nLr    262\nPb    207.2\nLi    6.941\nLu    174.967\nMG    24.30500\nMn    54.93805\nMt    266\nMd    258\nHg    200.59\nMo    95.94\nN     14.00700\nNA    22.98977\nNd    144.24\nNE    20.17970\nNp    237.048\nNi    58.6934\nNb    92.90638\nNo    259\nOs    190.2\nO     15.99900\nPd    106.42\nP     30.97400\nPt    195.08\nPu    244\nPo    209\nK     39.10200\nPr    140.90765\nPm    145\nPa    231.0359\nRa    226.025\nRn    222\nRe    186.207\nRh    102.9055\nRB    85.46780\nRu    101.07\nRf    261\nSm    150.36\nSc    44.95591\nSg    263\nSe    78.96\nSi    28.0855\nAg    107.8682\nNa    22.989768\nSr    87.62\nS     32.06000\nTa    180.9479\nTc    98\nTe    127.6\nTb    158.92534\nTl    204.3833\nTh    232.0381\nTm    168.93421\nSn    118.71\nTi    47.88\nW     183.85\nU     238.0289\nV     50.9415\nXe    131.29\nYb    173.04\nY     88.90585\nZN    65.37000\nZr    91.224\n'</em><a class="headerlink" href="#MDAnalysis.topology.tables.TABLE_MASSES" title="Permalink to this definition">¶</a></dt>
 <dd><p>Plain-text table with atomic masses in u.</p>
 </dd></dl>
 
@@ -154,7 +154,7 @@ <h1>4.21. MDAnalysis topology tables<a class="headerlink" href="#mdanalysis-topo
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -169,11 +169,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="core.html" title="4.20. Common functions for topology building — MDAnalysis.topology.core"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -183,7 +183,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/tpr_util.html b/package/doc/html/documentation_pages/topology/tpr_util.html
index 938807c9990..a5cf7449348 100644
--- a/package/doc/html/documentation_pages/topology/tpr_util.html
+++ b/package/doc/html/documentation_pages/topology/tpr_util.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4.22. Utility functions for the TPR topology parser &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4.22. Utility functions for the TPR topology parser &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="4. Topology modules" href="../topology_modules.html" />
     <link rel="next" title="5. Coordinates modules" href="../coordinates_modules.html" />
     <link rel="prev" title="4.21. MDAnalysis topology tables" href="tables.html" /> 
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+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
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@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="tables.html" title="4.21. MDAnalysis topology tables"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" accesskey="U">4. Topology modules</a> &raquo;</li> 
       </ul>
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         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
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   <h4>Next topic</h4>
   <p class="topless"><a href="../coordinates_modules.html"
                         title="next chapter">5. Coordinates modules</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/topology/tpr_util.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
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   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -101,20 +101,20 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="utility-functions-for-the-tpr-topology-parser">
 <h1>4.22. Utility functions for the TPR topology parser<a class="headerlink" href="#utility-functions-for-the-tpr-topology-parser" title="Permalink to this headline">¶</a></h1>
-<p>The <a class="reference internal" href="#module-MDAnalysis.topology.tpr" title="MDAnalysis.topology.tpr"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr</span></tt></a> module contains classes and
+<p>The <a class="reference internal" href="#module-MDAnalysis.topology.tpr" title="MDAnalysis.topology.tpr"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr</span></code></a> module contains classes and
 functions on which the Gromacs TPR topology reader
-<a class="reference internal" href="TPRParser.html#MDAnalysis.topology.TPRParser.TPRParser" title="MDAnalysis.topology.TPRParser.TPRParser"><tt class="xref py py-class docutils literal"><span class="pre">TPRParser</span></tt></a> is built.</p>
+<a class="reference internal" href="TPRParser.html#MDAnalysis.topology.TPRParser.TPRParser" title="MDAnalysis.topology.TPRParser.TPRParser"><code class="xref py py-class docutils literal"><span class="pre">TPRParser</span></code></a> is built.</p>
 <span class="target" id="module-MDAnalysis.topology.tpr"></span><div class="section" id="tpr-support">
 <h2>4.22.1. TPR support<a class="headerlink" href="#tpr-support" title="Permalink to this headline">¶</a></h2>
-<p>The <a class="reference internal" href="#module-MDAnalysis.topology.tpr" title="MDAnalysis.topology.tpr"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr</span></tt></a> module is required for the
-<a class="reference internal" href="TPRParser.html#module-MDAnalysis.topology.TPRParser" title="MDAnalysis.topology.TPRParser"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.TPRParser</span></tt></a> module.</p>
+<p>The <a class="reference internal" href="#module-MDAnalysis.topology.tpr" title="MDAnalysis.topology.tpr"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr</span></code></a> module is required for the
+<a class="reference internal" href="TPRParser.html#module-MDAnalysis.topology.TPRParser" title="MDAnalysis.topology.TPRParser"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.TPRParser</span></code></a> module.</p>
 <dl class="data">
 <dt id="MDAnalysis.topology.tpr.SUPPORTED_VERSIONS">
-<tt class="descclassname">MDAnalysis.topology.tpr.</tt><tt class="descname">SUPPORTED_VERSIONS</tt><em class="property"> = (58, 73, 83)</em><a class="headerlink" href="#MDAnalysis.topology.tpr.SUPPORTED_VERSIONS" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.</code><code class="descname">SUPPORTED_VERSIONS</code><em class="property"> = (58, 73, 83)</em><a class="headerlink" href="#MDAnalysis.topology.tpr.SUPPORTED_VERSIONS" title="Permalink to this definition">¶</a></dt>
 <dd><p>tuple() -&gt; empty tuple
 tuple(iterable) -&gt; tuple initialized from iterable&#8217;s items</p>
 <p>If the argument is a tuple, the return value is the same object.</p>
@@ -122,32 +122,32 @@ <h2>4.22.1. TPR support<a class="headerlink" href="#tpr-support" title="Permalin
 
 <p class="rubric">Sub-modules</p>
 <ul class="simple">
-<li><a class="reference internal" href="#module-MDAnalysis.topology.tpr.setting" title="MDAnalysis.topology.tpr.setting"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr.setting</span></tt></a></li>
-<li><a class="reference internal" href="#module-MDAnalysis.topology.tpr.obj" title="MDAnalysis.topology.tpr.obj"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr.obj</span></tt></a></li>
-<li><a class="reference internal" href="#module-MDAnalysis.topology.tpr.utils" title="MDAnalysis.topology.tpr.utils"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr.utils</span></tt></a></li>
+<li><a class="reference internal" href="#module-MDAnalysis.topology.tpr.setting" title="MDAnalysis.topology.tpr.setting"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr.setting</span></code></a></li>
+<li><a class="reference internal" href="#module-MDAnalysis.topology.tpr.obj" title="MDAnalysis.topology.tpr.obj"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr.obj</span></code></a></li>
+<li><a class="reference internal" href="#module-MDAnalysis.topology.tpr.utils" title="MDAnalysis.topology.tpr.utils"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.topology.tpr.utils</span></code></a></li>
 </ul>
 </div>
 <span class="target" id="module-MDAnalysis.topology.tpr.setting"></span><div class="section" id="tprparser-settings">
 <h2>4.22.2. TPRParser settings<a class="headerlink" href="#tprparser-settings" title="Permalink to this headline">¶</a></h2>
 <p>Definition of constants.</p>
 <p>The currently read file format versions are defined in
-<a class="reference internal" href="#MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS" title="MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS"><tt class="xref py py-data docutils literal"><span class="pre">SUPPORTED_VERSIONS</span></tt></a>.</p>
+<a class="reference internal" href="#MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS" title="MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS"><code class="xref py py-data docutils literal"><span class="pre">SUPPORTED_VERSIONS</span></code></a>.</p>
 <dl class="data">
 <dt id="MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS">
-<tt class="descclassname">MDAnalysis.topology.tpr.setting.</tt><tt class="descname">SUPPORTED_VERSIONS</tt><em class="property"> = (58, 73, 83)</em><a class="headerlink" href="#MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.setting.</code><code class="descname">SUPPORTED_VERSIONS</code><em class="property"> = (58, 73, 83)</em><a class="headerlink" href="#MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS" title="Permalink to this definition">¶</a></dt>
 <dd><p>Gromacs TPR file format versions that can be read by the TPRParser.</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.topology.tpr.setting.ftupd">
-<tt class="descclassname">MDAnalysis.topology.tpr.setting.</tt><tt class="descname">ftupd</tt><em class="property"> = [(20, 3), (20, 4), (20, 5), (34, 6), (43, 7), (43, 8), (70, 9), (76, 12), (30, 13), (30, 14), (30, 15), (34, 16), (43, 17), (26, 20), (26, 22), (43, 23), (65, 24), (60, 25), (61, 26), (61, 27), (72, 28), (72, 29), (41, 32), (41, 33), (32, 37), (32, 41), (32, 42), (46, 43), (30, 44), (36, 46), (22, 50), (22, 51), (22, 52), (26, 55), (26, 56), (49, 66), (50, 67), (46, 68), (20, 69), (46, 73), (69, 75), (66, 76), (54, 78), (76, 47), (79, 81), (79, 82), (79, 83), (79, 84), (79, 85), (54, 78)]</em><a class="headerlink" href="#MDAnalysis.topology.tpr.setting.ftupd" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function types from <tt class="docutils literal"><span class="pre">&lt;gromacs_dir&gt;/src/gmxlib/tpxio.c</span></tt></p>
+<code class="descclassname">MDAnalysis.topology.tpr.setting.</code><code class="descname">ftupd</code><em class="property"> = [(20, 3), (20, 4), (20, 5), (34, 6), (43, 7), (43, 8), (70, 9), (76, 12), (30, 13), (30, 14), (30, 15), (34, 16), (43, 17), (26, 20), (26, 22), (43, 23), (65, 24), (60, 25), (61, 26), (61, 27), (72, 28), (72, 29), (41, 32), (41, 33), (32, 37), (32, 41), (32, 42), (46, 43), (30, 44), (36, 46), (22, 50), (22, 51), (22, 52), (26, 55), (26, 56), (49, 66), (50, 67), (46, 68), (20, 69), (46, 73), (69, 75), (66, 76), (54, 78), (76, 47), (79, 81), (79, 82), (79, 83), (79, 84), (79, 85), (54, 78)]</em><a class="headerlink" href="#MDAnalysis.topology.tpr.setting.ftupd" title="Permalink to this definition">¶</a></dt>
+<dd><p>Function types from <code class="docutils literal"><span class="pre">&lt;gromacs_dir&gt;/src/gmxlib/tpxio.c</span></code></p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.topology.tpr.setting.interaction_types">
-<tt class="descclassname">MDAnalysis.topology.tpr.setting.</tt><tt class="descname">interaction_types</tt><em class="property"> = [('BONDS', 'Bond', 2), ('G96BONDS', 'G96Bond', 2), ('MORSE', 'Morse', 2), ('CUBICBONDS', 'Cubic Bonds', 2), ('CONNBONDS', 'Connect Bonds', 2), ('HARMONIC', 'Harmonic Pot.', 2), ('FENEBONDS', 'FENE Bonds', 2), ('TABBONDS', 'Tab. Bonds', 2), ('TABBONDSNC', 'Tab. Bonds NC', 2), ('RESTRAINTPOT', 'Restraint Pot.', 2), ('ANGLES', 'Angle', 3), ('G96ANGLES', 'G96Angle', 3), ('LINEAR_ANGLES', 'Lin. Angle', 3), ('CROSS_BOND_BOND', 'Bond-Cross', 3), ('CROSS_BOND_ANGLE', 'BA-Cross', 3), ('UREY_BRADLEY', 'U-B', 3), ('QANGLES', 'Quartic Angles', 3), ('TABANGLES', 'Tab. Angles', 3), ('PDIHS', 'Proper Dih.', 4), ('RBDIHS', 'Ryckaert-Bell.', 4), ('FOURDIHS', 'Fourier Dih.', 4), ('IDIHS', 'Improper Dih.', 4), ('PIDIHS', 'Improper Dih.', 4), ('TABDIHS', 'Tab. Dih.', 4), ('CMAP', 'CMAP Dih.', 5), ('GB12', 'GB 1-2 Pol.', 2), ('GB13', 'GB 1-3 Pol.', 2), ('GB14', 'GB 1-4 Pol.', 2), ('GBPOL', 'GB Polarization', None), ('NPSOLVATION', 'Nonpolar Sol.', None), ('LJ14', 'LJ-14', 2), ('COUL14', 'Coulomb-14', None), ('LJC14_Q', 'LJC-14 q', 2), ('LJC_NB', 'LJC Pairs NB', 2), ('LJ_SR', 'LJ (SR)', 2), ('BHAM', 'Buck.ham (SR)', 2), ('LJ_LR', 'LJ (LR)', None), ('BHAM_LR', 'Buck.ham (LR)', None), ('DISPCORR', 'Disper. corr.', None), ('COUL_SR', 'Coulomb (SR)', None), ('COUL_LR', 'Coulomb (LR)', None), ('RF_EXCL', 'RF excl.', None), ('COUL_RECIP', 'Coul. recip.', None), ('DPD', 'DPD', None), ('POLARIZATION', 'Polarization', 2), ('WATERPOL', 'Water Pol.', 5), ('THOLE', 'Thole Pol.', 4), ('ANHARM_POL', 'Anharm. Pol.', 2), ('POSRES', 'Position Rest.', 1), ('DISRES', 'Dis. Rest.', 2), ('DISRESVIOL', 'D.R.Viol. (nm)', None), ('ORIRES', 'Orient. Rest.', 2), ('ORDEV', 'Ori. R. RMSD', None), ('ANGRES', 'Angle Rest.', 4), ('ANGRESZ', 'Angle Rest. Z', 2), ('DIHRES', 'Dih. Rest.', 4), ('DIHRESVIOL', 'Dih. Rest. Viol.', None), ('CONSTR', 'Constraint', 2), ('CONSTRNC', 'Constr. No Conn.', 2), ('SETTLE', 'Settle', 3), ('VSITE2', 'Virtual site 2', 3), ('VSITE3', 'Virtual site 3', 4), ('VSITE3FD', 'Virtual site 3fd', 4), ('VSITE3FAD', 'Virtual site 3fad', 4), ('VSITE3OUT', 'Virtual site 3out', 4), ('VSITE4FD', 'Virtual site 4fd', 5), ('VSITE4FDN', 'Virtual site 4fdn', 5), ('VSITEN', 'Virtual site N', 2), ('COM_PULL', 'COM Pull En.', None), ('EQM', 'Quantum En.', None), ('EPOT', 'Potential', None), ('EKIN', 'Kinetic En.', None), ('ETOT', 'Total Energy', None), ('ECONS', 'Conserved En.', None), ('TEMP', 'Temperature', None), ('VTEMP', 'Vir. Temp. (not used)', None), ('PDISPCORR', 'Pres. DC', None), ('PRES', 'Pressure', None), ('DH/DL_CON', 'dH/dl constr.', None), ('DV/DL', 'dVremain/dl', None), ('DK/DL', 'dEkin/dl', None), ('DVC/DL', 'dVcoul/dl', None), ('DVV/DL', 'dVvdw/dl', None), ('DVB/DL', 'dVbonded/dl', None), ('DVR/DL', 'dVrestraint/dl', None), ('DVT/DL', 'dVtemperature/dl', None)]</em><a class="headerlink" href="#MDAnalysis.topology.tpr.setting.interaction_types" title="Permalink to this definition">¶</a></dt>
-<dd><p>Interaction types from <tt class="docutils literal"><span class="pre">&lt;gromacs_dir&gt;/gmxlib/ifunc.c</span></tt></p>
+<code class="descclassname">MDAnalysis.topology.tpr.setting.</code><code class="descname">interaction_types</code><em class="property"> = [('BONDS', 'Bond', 2), ('G96BONDS', 'G96Bond', 2), ('MORSE', 'Morse', 2), ('CUBICBONDS', 'Cubic Bonds', 2), ('CONNBONDS', 'Connect Bonds', 2), ('HARMONIC', 'Harmonic Pot.', 2), ('FENEBONDS', 'FENE Bonds', 2), ('TABBONDS', 'Tab. Bonds', 2), ('TABBONDSNC', 'Tab. Bonds NC', 2), ('RESTRAINTPOT', 'Restraint Pot.', 2), ('ANGLES', 'Angle', 3), ('G96ANGLES', 'G96Angle', 3), ('LINEAR_ANGLES', 'Lin. Angle', 3), ('CROSS_BOND_BOND', 'Bond-Cross', 3), ('CROSS_BOND_ANGLE', 'BA-Cross', 3), ('UREY_BRADLEY', 'U-B', 3), ('QANGLES', 'Quartic Angles', 3), ('TABANGLES', 'Tab. Angles', 3), ('PDIHS', 'Proper Dih.', 4), ('RBDIHS', 'Ryckaert-Bell.', 4), ('FOURDIHS', 'Fourier Dih.', 4), ('IDIHS', 'Improper Dih.', 4), ('PIDIHS', 'Improper Dih.', 4), ('TABDIHS', 'Tab. Dih.', 4), ('CMAP', 'CMAP Dih.', 5), ('GB12', 'GB 1-2 Pol.', 2), ('GB13', 'GB 1-3 Pol.', 2), ('GB14', 'GB 1-4 Pol.', 2), ('GBPOL', 'GB Polarization', None), ('NPSOLVATION', 'Nonpolar Sol.', None), ('LJ14', 'LJ-14', 2), ('COUL14', 'Coulomb-14', None), ('LJC14_Q', 'LJC-14 q', 2), ('LJC_NB', 'LJC Pairs NB', 2), ('LJ_SR', 'LJ (SR)', 2), ('BHAM', 'Buck.ham (SR)', 2), ('LJ_LR', 'LJ (LR)', None), ('BHAM_LR', 'Buck.ham (LR)', None), ('DISPCORR', 'Disper. corr.', None), ('COUL_SR', 'Coulomb (SR)', None), ('COUL_LR', 'Coulomb (LR)', None), ('RF_EXCL', 'RF excl.', None), ('COUL_RECIP', 'Coul. recip.', None), ('DPD', 'DPD', None), ('POLARIZATION', 'Polarization', 2), ('WATERPOL', 'Water Pol.', 5), ('THOLE', 'Thole Pol.', 4), ('ANHARM_POL', 'Anharm. Pol.', 2), ('POSRES', 'Position Rest.', 1), ('DISRES', 'Dis. Rest.', 2), ('DISRESVIOL', 'D.R.Viol. (nm)', None), ('ORIRES', 'Orient. Rest.', 2), ('ORDEV', 'Ori. R. RMSD', None), ('ANGRES', 'Angle Rest.', 4), ('ANGRESZ', 'Angle Rest. Z', 2), ('DIHRES', 'Dih. Rest.', 4), ('DIHRESVIOL', 'Dih. Rest. Viol.', None), ('CONSTR', 'Constraint', 2), ('CONSTRNC', 'Constr. No Conn.', 2), ('SETTLE', 'Settle', 3), ('VSITE2', 'Virtual site 2', 3), ('VSITE3', 'Virtual site 3', 4), ('VSITE3FD', 'Virtual site 3fd', 4), ('VSITE3FAD', 'Virtual site 3fad', 4), ('VSITE3OUT', 'Virtual site 3out', 4), ('VSITE4FD', 'Virtual site 4fd', 5), ('VSITE4FDN', 'Virtual site 4fdn', 5), ('VSITEN', 'Virtual site N', 2), ('COM_PULL', 'COM Pull En.', None), ('EQM', 'Quantum En.', None), ('EPOT', 'Potential', None), ('EKIN', 'Kinetic En.', None), ('ETOT', 'Total Energy', None), ('ECONS', 'Conserved En.', None), ('TEMP', 'Temperature', None), ('VTEMP', 'Vir. Temp. (not used)', None), ('PDISPCORR', 'Pres. DC', None), ('PRES', 'Pressure', None), ('DH/DL_CON', 'dH/dl constr.', None), ('DV/DL', 'dVremain/dl', None), ('DK/DL', 'dEkin/dl', None), ('DVC/DL', 'dVcoul/dl', None), ('DVV/DL', 'dVvdw/dl', None), ('DVB/DL', 'dVbonded/dl', None), ('DVR/DL', 'dVrestraint/dl', None), ('DVT/DL', 'dVtemperature/dl', None)]</em><a class="headerlink" href="#MDAnalysis.topology.tpr.setting.interaction_types" title="Permalink to this definition">¶</a></dt>
+<dd><p>Interaction types from <code class="docutils literal"><span class="pre">&lt;gromacs_dir&gt;/gmxlib/ifunc.c</span></code></p>
 </dd></dl>
 
 </div>
@@ -155,59 +155,58 @@ <h2>4.22.2. TPRParser settings<a class="headerlink" href="#tprparser-settings" t
 <h2>4.22.3. Class definitions for the TPRParser<a class="headerlink" href="#class-definitions-for-the-tprparser" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.Atom">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">Atom</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom" title="Permalink to this definition">¶</a></dt>
-<dd><p>Atom(m, q, mB, qB, tp, typeB, ptype, resind, atomnumber)</p>
-<dl class="attribute">
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">Atom</code><span class="sig-paren">(</span><em>m</em>, <em>q</em>, <em>mB</em>, <em>qB</em>, <em>tp</em>, <em>typeB</em>, <em>ptype</em>, <em>resind</em>, <em>atomnumber</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atom.atomnumber">
-<tt class="descname">atomnumber</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.atomnumber" title="Permalink to this definition">¶</a></dt>
+<code class="descname">atomnumber</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.atomnumber" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 8</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atom.m">
-<tt class="descname">m</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.m" title="Permalink to this definition">¶</a></dt>
+<code class="descname">m</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.m" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 0</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atom.mB">
-<tt class="descname">mB</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.mB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">mB</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.mB" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 2</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atom.ptype">
-<tt class="descname">ptype</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.ptype" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ptype</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.ptype" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 6</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atom.q">
-<tt class="descname">q</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.q" title="Permalink to this definition">¶</a></dt>
+<code class="descname">q</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.q" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 1</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atom.qB">
-<tt class="descname">qB</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.qB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">qB</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.qB" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 3</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atom.resind">
-<tt class="descname">resind</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.resind" title="Permalink to this definition">¶</a></dt>
+<code class="descname">resind</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.resind" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 7</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atom.tp">
-<tt class="descname">tp</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.tp" title="Permalink to this definition">¶</a></dt>
+<code class="descname">tp</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.tp" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 4</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atom.typeB">
-<tt class="descname">typeB</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.typeB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">typeB</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atom.typeB" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 5</p>
 </dd></dl>
 
@@ -215,52 +214,51 @@ <h2>4.22.3. Class definitions for the TPRParser<a class="headerlink" href="#clas
 
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.AtomKind">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">AtomKind</tt><big>(</big><em>id</em>, <em>name</em>, <em>type</em>, <em>resid</em>, <em>resname</em>, <em>mass</em>, <em>charge</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#AtomKind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.AtomKind" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">AtomKind</code><span class="sig-paren">(</span><em>id</em>, <em>name</em>, <em>type</em>, <em>resid</em>, <em>resname</em>, <em>mass</em>, <em>charge</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#AtomKind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.AtomKind" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.Atoms">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">Atoms</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms" title="Permalink to this definition">¶</a></dt>
-<dd><p>Atoms(atoms, nr, nres, type, typeB, atomnames, resnames)</p>
-<dl class="attribute">
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">Atoms</code><span class="sig-paren">(</span><em>atoms</em>, <em>nr</em>, <em>nres</em>, <em>type</em>, <em>typeB</em>, <em>atomnames</em>, <em>resnames</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atoms.atomnames">
-<tt class="descname">atomnames</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.atomnames" title="Permalink to this definition">¶</a></dt>
+<code class="descname">atomnames</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.atomnames" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 5</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atoms.atoms">
-<tt class="descname">atoms</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">atoms</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 0</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atoms.nr">
-<tt class="descname">nr</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.nr" title="Permalink to this definition">¶</a></dt>
+<code class="descname">nr</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.nr" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 1</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atoms.nres">
-<tt class="descname">nres</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.nres" title="Permalink to this definition">¶</a></dt>
+<code class="descname">nres</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.nres" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 2</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atoms.resnames">
-<tt class="descname">resnames</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.resnames" title="Permalink to this definition">¶</a></dt>
+<code class="descname">resnames</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.resnames" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 6</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atoms.type">
-<tt class="descname">type</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.type" title="Permalink to this definition">¶</a></dt>
+<code class="descname">type</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.type" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 3</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Atoms.typeB">
-<tt class="descname">typeB</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.typeB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">typeB</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Atoms.typeB" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 4</p>
 </dd></dl>
 
@@ -268,23 +266,22 @@ <h2>4.22.3. Class definitions for the TPRParser<a class="headerlink" href="#clas
 
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.Box">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">Box</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Box" title="Permalink to this definition">¶</a></dt>
-<dd><p>Box(size, rel, v)</p>
-<dl class="attribute">
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">Box</code><span class="sig-paren">(</span><em>size</em>, <em>rel</em>, <em>v</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Box" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Box.rel">
-<tt class="descname">rel</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Box.rel" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rel</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Box.rel" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 1</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Box.size">
-<tt class="descname">size</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Box.size" title="Permalink to this definition">¶</a></dt>
+<code class="descname">size</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Box.size" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 0</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Box.v">
-<tt class="descname">v</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Box.v" title="Permalink to this definition">¶</a></dt>
+<code class="descname">v</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Box.v" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 2</p>
 </dd></dl>
 
@@ -292,23 +289,22 @@ <h2>4.22.3. Class definitions for the TPRParser<a class="headerlink" href="#clas
 
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.Ilist">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">Ilist</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Ilist" title="Permalink to this definition">¶</a></dt>
-<dd><p>Ilist(nr, ik, iatoms)</p>
-<dl class="attribute">
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">Ilist</code><span class="sig-paren">(</span><em>nr</em>, <em>ik</em>, <em>iatoms</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Ilist" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Ilist.iatoms">
-<tt class="descname">iatoms</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Ilist.iatoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">iatoms</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Ilist.iatoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 2</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Ilist.ik">
-<tt class="descname">ik</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Ilist.ik" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ik</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Ilist.ik" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 1</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Ilist.nr">
-<tt class="descname">nr</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Ilist.nr" title="Permalink to this definition">¶</a></dt>
+<code class="descname">nr</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Ilist.nr" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 0</p>
 </dd></dl>
 
@@ -316,46 +312,45 @@ <h2>4.22.3. Class definitions for the TPRParser<a class="headerlink" href="#clas
 
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.InteractionKind">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">InteractionKind</tt><big>(</big><em>name</em>, <em>long_name</em>, <em>natoms</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#InteractionKind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.InteractionKind" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">InteractionKind</code><span class="sig-paren">(</span><em>name</em>, <em>long_name</em>, <em>natoms</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#InteractionKind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.InteractionKind" title="Permalink to this definition">¶</a></dt>
 <dd><p>natoms: number of atoms involved in this type of interaction</p>
 <dl class="method">
 <dt id="MDAnalysis.topology.tpr.obj.InteractionKind.process">
-<tt class="descname">process</tt><big>(</big><em>atom_ndx</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#InteractionKind.process"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.InteractionKind.process" title="Permalink to this definition">¶</a></dt>
+<code class="descname">process</code><span class="sig-paren">(</span><em>atom_ndx</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#InteractionKind.process"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.InteractionKind.process" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.Molblock">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">Molblock</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock" title="Permalink to this definition">¶</a></dt>
-<dd><p>Molblock(molb_type, molb_nmol, molb_natoms_mol, molb_nposres_xA, molb_nposres_xB)</p>
-<dl class="attribute">
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">Molblock</code><span class="sig-paren">(</span><em>molb_type</em>, <em>molb_nmol</em>, <em>molb_natoms_mol</em>, <em>molb_nposres_xA</em>, <em>molb_nposres_xB</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Molblock.molb_natoms_mol">
-<tt class="descname">molb_natoms_mol</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock.molb_natoms_mol" title="Permalink to this definition">¶</a></dt>
+<code class="descname">molb_natoms_mol</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock.molb_natoms_mol" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 2</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Molblock.molb_nmol">
-<tt class="descname">molb_nmol</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock.molb_nmol" title="Permalink to this definition">¶</a></dt>
+<code class="descname">molb_nmol</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock.molb_nmol" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 1</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xA">
-<tt class="descname">molb_nposres_xA</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xA" title="Permalink to this definition">¶</a></dt>
+<code class="descname">molb_nposres_xA</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xA" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 3</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xB">
-<tt class="descname">molb_nposres_xB</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">molb_nposres_xB</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xB" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 4</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Molblock.molb_type">
-<tt class="descname">molb_type</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock.molb_type" title="Permalink to this definition">¶</a></dt>
+<code class="descname">molb_type</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Molblock.molb_type" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 0</p>
 </dd></dl>
 
@@ -363,58 +358,57 @@ <h2>4.22.3. Class definitions for the TPRParser<a class="headerlink" href="#clas
 
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.MoleculeKind">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">MoleculeKind</tt><big>(</big><em>name</em>, <em>atomkinds</em>, <em>bonds=None</em>, <em>angles=None</em>, <em>dihe=None</em>, <em>impr=None</em>, <em>donors=None</em>, <em>acceptors=None</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">MoleculeKind</code><span class="sig-paren">(</span><em>name</em>, <em>atomkinds</em>, <em>bonds=None</em>, <em>angles=None</em>, <em>dihe=None</em>, <em>impr=None</em>, <em>donors=None</em>, <em>acceptors=None</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind" title="Permalink to this definition">¶</a></dt>
 <dd><dl class="method">
 <dt id="MDAnalysis.topology.tpr.obj.MoleculeKind.number_of_atoms">
-<tt class="descname">number_of_atoms</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.number_of_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.number_of_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">number_of_atoms</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.number_of_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.number_of_atoms" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.tpr.obj.MoleculeKind.number_of_residues">
-<tt class="descname">number_of_residues</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.number_of_residues"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.number_of_residues" title="Permalink to this definition">¶</a></dt>
+<code class="descname">number_of_residues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.number_of_residues"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.number_of_residues" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.tpr.obj.MoleculeKind.remap_angles">
-<tt class="descname">remap_angles</tt><big>(</big><em>atom_start_ndx</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.remap_angles"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.remap_angles" title="Permalink to this definition">¶</a></dt>
+<code class="descname">remap_angles</code><span class="sig-paren">(</span><em>atom_start_ndx</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.remap_angles"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.remap_angles" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.tpr.obj.MoleculeKind.remap_bonds">
-<tt class="descname">remap_bonds</tt><big>(</big><em>atom_start_ndx</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.remap_bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.remap_bonds" title="Permalink to this definition">¶</a></dt>
+<code class="descname">remap_bonds</code><span class="sig-paren">(</span><em>atom_start_ndx</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.remap_bonds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.remap_bonds" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.tpr.obj.MoleculeKind.remap_dihe">
-<tt class="descname">remap_dihe</tt><big>(</big><em>atom_start_ndx</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.remap_dihe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.remap_dihe" title="Permalink to this definition">¶</a></dt>
+<code class="descname">remap_dihe</code><span class="sig-paren">(</span><em>atom_start_ndx</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.remap_dihe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.remap_dihe" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="method">
 <dt id="MDAnalysis.topology.tpr.obj.MoleculeKind.remap_impr">
-<tt class="descname">remap_impr</tt><big>(</big><em>atom_start_ndx</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.remap_impr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.remap_impr" title="Permalink to this definition">¶</a></dt>
+<code class="descname">remap_impr</code><span class="sig-paren">(</span><em>atom_start_ndx</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/obj.html#MoleculeKind.remap_impr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.MoleculeKind.remap_impr" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
 
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.Mtop">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">Mtop</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Mtop" title="Permalink to this definition">¶</a></dt>
-<dd><p>Mtop(nmoltype, moltypes, nmolblock)</p>
-<dl class="attribute">
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">Mtop</code><span class="sig-paren">(</span><em>nmoltype</em>, <em>moltypes</em>, <em>nmolblock</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Mtop" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Mtop.moltypes">
-<tt class="descname">moltypes</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Mtop.moltypes" title="Permalink to this definition">¶</a></dt>
+<code class="descname">moltypes</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Mtop.moltypes" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 1</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Mtop.nmolblock">
-<tt class="descname">nmolblock</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Mtop.nmolblock" title="Permalink to this definition">¶</a></dt>
+<code class="descname">nmolblock</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Mtop.nmolblock" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 2</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Mtop.nmoltype">
-<tt class="descname">nmoltype</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Mtop.nmoltype" title="Permalink to this definition">¶</a></dt>
+<code class="descname">nmoltype</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Mtop.nmoltype" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 0</p>
 </dd></dl>
 
@@ -422,41 +416,40 @@ <h2>4.22.3. Class definitions for the TPRParser<a class="headerlink" href="#clas
 
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.Params">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">Params</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params" title="Permalink to this definition">¶</a></dt>
-<dd><p>Params(atnr, ntypes, functype, reppow, fudgeQQ, iparams)</p>
-<dl class="attribute">
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">Params</code><span class="sig-paren">(</span><em>atnr</em>, <em>ntypes</em>, <em>functype</em>, <em>reppow</em>, <em>fudgeQQ</em>, <em>iparams</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Params.atnr">
-<tt class="descname">atnr</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.atnr" title="Permalink to this definition">¶</a></dt>
+<code class="descname">atnr</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.atnr" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 0</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Params.fudgeQQ">
-<tt class="descname">fudgeQQ</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.fudgeQQ" title="Permalink to this definition">¶</a></dt>
+<code class="descname">fudgeQQ</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.fudgeQQ" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 4</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Params.functype">
-<tt class="descname">functype</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.functype" title="Permalink to this definition">¶</a></dt>
+<code class="descname">functype</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.functype" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 2</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Params.iparams">
-<tt class="descname">iparams</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.iparams" title="Permalink to this definition">¶</a></dt>
+<code class="descname">iparams</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.iparams" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 5</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Params.ntypes">
-<tt class="descname">ntypes</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.ntypes" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ntypes</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.ntypes" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 1</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.Params.reppow">
-<tt class="descname">reppow</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.reppow" title="Permalink to this definition">¶</a></dt>
+<code class="descname">reppow</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.Params.reppow" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 3</p>
 </dd></dl>
 
@@ -464,35 +457,34 @@ <h2>4.22.3. Class definitions for the TPRParser<a class="headerlink" href="#clas
 
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.TPRTopology">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">TPRTopology</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology" title="Permalink to this definition">¶</a></dt>
-<dd><p>TPRTopology(atoms, bonds, angles, dihe, impr)</p>
-<dl class="attribute">
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">TPRTopology</code><span class="sig-paren">(</span><em>atoms</em>, <em>bonds</em>, <em>angles</em>, <em>dihe</em>, <em>impr</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TPRTopology.angles">
-<tt class="descname">angles</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology.angles" title="Permalink to this definition">¶</a></dt>
+<code class="descname">angles</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology.angles" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 2</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TPRTopology.atoms">
-<tt class="descname">atoms</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology.atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">atoms</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology.atoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 0</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TPRTopology.bonds">
-<tt class="descname">bonds</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology.bonds" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bonds</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology.bonds" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 1</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TPRTopology.dihe">
-<tt class="descname">dihe</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology.dihe" title="Permalink to this definition">¶</a></dt>
+<code class="descname">dihe</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology.dihe" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 3</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TPRTopology.impr">
-<tt class="descname">impr</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology.impr" title="Permalink to this definition">¶</a></dt>
+<code class="descname">impr</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TPRTopology.impr" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 4</p>
 </dd></dl>
 
@@ -500,101 +492,100 @@ <h2>4.22.3. Class definitions for the TPRParser<a class="headerlink" href="#clas
 
 <dl class="class">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader">
-<em class="property">class </em><tt class="descclassname">MDAnalysis.topology.tpr.obj.</tt><tt class="descname">TpxHeader</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader" title="Permalink to this definition">¶</a></dt>
-<dd><p>TpxHeader(number, ver_str, precision, fver, fgen, file_tag, natoms, ngtc, fep_state, lamb, bIr, bTop, bX, bV, bF, bBox)</p>
-<dl class="attribute">
+<em class="property">class </em><code class="descclassname">MDAnalysis.topology.tpr.obj.</code><code class="descname">TpxHeader</code><span class="sig-paren">(</span><em>number</em>, <em>ver_str</em>, <em>precision</em>, <em>fver</em>, <em>fgen</em>, <em>file_tag</em>, <em>natoms</em>, <em>ngtc</em>, <em>fep_state</em>, <em>lamb</em>, <em>bIr</em>, <em>bTop</em>, <em>bX</em>, <em>bV</em>, <em>bF</em>, <em>bBox</em><span class="sig-paren">)</span><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.bBox">
-<tt class="descname">bBox</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bBox" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bBox</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bBox" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 15</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.bF">
-<tt class="descname">bF</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bF" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bF</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bF" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 14</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.bIr">
-<tt class="descname">bIr</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bIr" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bIr</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bIr" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 10</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.bTop">
-<tt class="descname">bTop</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bTop" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bTop</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bTop" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 11</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.bV">
-<tt class="descname">bV</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bV" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bV</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bV" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 13</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.bX">
-<tt class="descname">bX</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bX" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bX</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.bX" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 12</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.fep_state">
-<tt class="descname">fep_state</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.fep_state" title="Permalink to this definition">¶</a></dt>
+<code class="descname">fep_state</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.fep_state" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 8</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.fgen">
-<tt class="descname">fgen</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.fgen" title="Permalink to this definition">¶</a></dt>
+<code class="descname">fgen</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.fgen" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 4</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.file_tag">
-<tt class="descname">file_tag</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.file_tag" title="Permalink to this definition">¶</a></dt>
+<code class="descname">file_tag</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.file_tag" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 5</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.fver">
-<tt class="descname">fver</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.fver" title="Permalink to this definition">¶</a></dt>
+<code class="descname">fver</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.fver" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 3</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.lamb">
-<tt class="descname">lamb</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.lamb" title="Permalink to this definition">¶</a></dt>
+<code class="descname">lamb</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.lamb" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 9</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.natoms">
-<tt class="descname">natoms</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.natoms" title="Permalink to this definition">¶</a></dt>
+<code class="descname">natoms</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.natoms" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 6</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.ngtc">
-<tt class="descname">ngtc</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.ngtc" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ngtc</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.ngtc" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 7</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.number">
-<tt class="descname">number</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.number" title="Permalink to this definition">¶</a></dt>
+<code class="descname">number</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.number" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 0</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.precision">
-<tt class="descname">precision</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.precision" title="Permalink to this definition">¶</a></dt>
+<code class="descname">precision</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.precision" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 2</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="MDAnalysis.topology.tpr.obj.TpxHeader.ver_str">
-<tt class="descname">ver_str</tt><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.ver_str" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ver_str</code><a class="headerlink" href="#MDAnalysis.topology.tpr.obj.TpxHeader.ver_str" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 1</p>
 </dd></dl>
 
@@ -604,7 +595,7 @@ <h2>4.22.3. Class definitions for the TPRParser<a class="headerlink" href="#clas
 <span class="target" id="module-MDAnalysis.topology.tpr.utils"></span><div class="section" id="utilities-for-the-tprparser">
 <h2>4.22.4. Utilities for the TPRParser<a class="headerlink" href="#utilities-for-the-tprparser" title="Permalink to this headline">¶</a></h2>
 <p>Function calling order:</p>
-<div class="highlight-python"><pre>(TPRParser.py call do_mtop)
+<div class="highlight-python"><div class="highlight"><pre>(TPRParser.py call do_mtop)
 do_mtop -&gt; do_symtab
         -&gt; do_ffparams -&gt; do_iparams
         -&gt; do_moltype  -&gt; do_atoms  -&gt; do_atom
@@ -612,69 +603,70 @@ <h2>4.22.4. Utilities for the TPRParser<a class="headerlink" href="#utilities-fo
                        -&gt; do_ilists
                        -&gt; do_block
                        -&gt; do_blocka
-        -&gt; do_molblock</pre>
+        -&gt; do_molblock
+</pre></div>
 </div>
-<p>Then compose the stuffs in the format <tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></tt> reads in.</p>
-<p>The module also contains the <a class="reference internal" href="#MDAnalysis.topology.tpr.utils.do_inputrec" title="MDAnalysis.topology.tpr.utils.do_inputrec"><tt class="xref py py-func docutils literal"><span class="pre">do_inputrec()</span></tt></a> to read the TPR header with.</p>
+<p>Then compose the stuffs in the format <code class="xref py py-class docutils literal"><span class="pre">MDAnalysis.Universe</span></code> reads in.</p>
+<p>The module also contains the <a class="reference internal" href="#MDAnalysis.topology.tpr.utils.do_inputrec" title="MDAnalysis.topology.tpr.utils.do_inputrec"><code class="xref py py-func docutils literal"><span class="pre">do_inputrec()</span></code></a> to read the TPR header with.</p>
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.define_unpack_real">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">define_unpack_real</tt><big>(</big><em>prec</em>, <em>data</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#define_unpack_real"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.define_unpack_real" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">define_unpack_real</code><span class="sig-paren">(</span><em>prec</em>, <em>data</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#define_unpack_real"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.define_unpack_real" title="Permalink to this definition">¶</a></dt>
 <dd><p>Define an unpack_real method of data based on the float precision used</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_atom">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_atom</tt><big>(</big><em>data</em>, <em>fver</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_atom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_atom" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_atom</code><span class="sig-paren">(</span><em>data</em>, <em>fver</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_atom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_atom" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_atoms">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_atoms</tt><big>(</big><em>data</em>, <em>symtab</em>, <em>fver</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_atoms" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_atoms</code><span class="sig-paren">(</span><em>data</em>, <em>symtab</em>, <em>fver</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_atoms" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_atomtypes">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_atomtypes</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_atomtypes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_atomtypes" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_atomtypes</code><span class="sig-paren">(</span><em>data</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_atomtypes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_atomtypes" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_block">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_block</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_block"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_block" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_block</code><span class="sig-paren">(</span><em>data</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_block"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_block" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_blocka">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_blocka</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_blocka"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_blocka" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_blocka</code><span class="sig-paren">(</span><em>data</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_blocka"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_blocka" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_ffparams">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_ffparams</tt><big>(</big><em>data</em>, <em>fver</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_ffparams"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_ffparams" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_ffparams</code><span class="sig-paren">(</span><em>data</em>, <em>fver</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_ffparams"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_ffparams" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_groups">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_groups</tt><big>(</big><em>data</em>, <em>symtab</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_groups"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_groups" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_groups</code><span class="sig-paren">(</span><em>data</em>, <em>symtab</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_groups"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_groups" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_grps">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_grps</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_grps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_grps" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_grps</code><span class="sig-paren">(</span><em>data</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_grps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_grps" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_harm">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_harm</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_harm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_harm" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_harm</code><span class="sig-paren">(</span><em>data</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_harm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_harm" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_ilists">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_ilists</tt><big>(</big><em>data</em>, <em>fver</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_ilists"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_ilists" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_ilists</code><span class="sig-paren">(</span><em>data</em>, <em>fver</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_ilists"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_ilists" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_inputrec">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_inputrec</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_inputrec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_inputrec" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_inputrec</code><span class="sig-paren">(</span><em>data</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_inputrec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_inputrec" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read through header information from TPR file <em>data</em> structure.</p>
 <p>Note that this function does not return any useful data itself. If
 your are interested in using the header information, use this
@@ -683,81 +675,81 @@ <h2>4.22.4. Utilities for the TPRParser<a class="headerlink" href="#utilities-fo
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_iparams">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_iparams</tt><big>(</big><em>data</em>, <em>functypes</em>, <em>fver</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_iparams"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_iparams" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_iparams</code><span class="sig-paren">(</span><em>data</em>, <em>functypes</em>, <em>fver</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_iparams"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_iparams" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_molblock">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_molblock</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_molblock"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_molblock" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_molblock</code><span class="sig-paren">(</span><em>data</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_molblock"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_molblock" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_moltype">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_moltype</tt><big>(</big><em>data</em>, <em>symtab</em>, <em>fver</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_moltype"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_moltype" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_moltype</code><span class="sig-paren">(</span><em>data</em>, <em>symtab</em>, <em>fver</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_moltype"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_moltype" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_mtop">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_mtop</tt><big>(</big><em>data</em>, <em>fver</em>, <em>u</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_mtop"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_mtop" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_mtop</code><span class="sig-paren">(</span><em>data</em>, <em>fver</em>, <em>u</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_mtop"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_mtop" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_resinfo">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_resinfo</tt><big>(</big><em>data</em>, <em>symtab</em>, <em>fver</em>, <em>nres</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_resinfo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_resinfo" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_resinfo</code><span class="sig-paren">(</span><em>data</em>, <em>symtab</em>, <em>fver</em>, <em>nres</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_resinfo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_resinfo" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_rvec">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_rvec</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_rvec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_rvec" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_rvec</code><span class="sig-paren">(</span><em>data</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_rvec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_rvec" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_symstr">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_symstr</tt><big>(</big><em>data</em>, <em>symtab</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_symstr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_symstr" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_symstr</code><span class="sig-paren">(</span><em>data</em>, <em>symtab</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_symstr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_symstr" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.do_symtab">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">do_symtab</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_symtab"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_symtab" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">do_symtab</code><span class="sig-paren">(</span><em>data</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#do_symtab"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.do_symtab" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.extract_box_info">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">extract_box_info</tt><big>(</big><em>data</em>, <em>fver</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#extract_box_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.extract_box_info" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">extract_box_info</code><span class="sig-paren">(</span><em>data</em>, <em>fver</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#extract_box_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.extract_box_info" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.fver_err">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">fver_err</tt><big>(</big><em>fver</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#fver_err"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.fver_err" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">fver_err</code><span class="sig-paren">(</span><em>fver</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#fver_err"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.fver_err" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.ndo_int">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">ndo_int</tt><big>(</big><em>data</em>, <em>n</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#ndo_int"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.ndo_int" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">ndo_int</code><span class="sig-paren">(</span><em>data</em>, <em>n</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#ndo_int"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.ndo_int" title="Permalink to this definition">¶</a></dt>
 <dd><p>mimic of gmx_fio_ndo_real in gromacs</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.ndo_ivec">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">ndo_ivec</tt><big>(</big><em>data</em>, <em>n</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#ndo_ivec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.ndo_ivec" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">ndo_ivec</code><span class="sig-paren">(</span><em>data</em>, <em>n</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#ndo_ivec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.ndo_ivec" title="Permalink to this definition">¶</a></dt>
 <dd><p>mimic of gmx_fio_ndo_rvec in gromacs</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.ndo_real">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">ndo_real</tt><big>(</big><em>data</em>, <em>n</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#ndo_real"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.ndo_real" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">ndo_real</code><span class="sig-paren">(</span><em>data</em>, <em>n</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#ndo_real"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.ndo_real" title="Permalink to this definition">¶</a></dt>
 <dd><p>mimic of gmx_fio_ndo_real in gromacs</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.ndo_rvec">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">ndo_rvec</tt><big>(</big><em>data</em>, <em>n</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#ndo_rvec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.ndo_rvec" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">ndo_rvec</code><span class="sig-paren">(</span><em>data</em>, <em>n</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#ndo_rvec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.ndo_rvec" title="Permalink to this definition">¶</a></dt>
 <dd><p>mimic of gmx_fio_ndo_rvec in gromacs</p>
 </dd></dl>
 
 <dl class="function">
 <dt id="MDAnalysis.topology.tpr.utils.read_tpxheader">
-<tt class="descclassname">MDAnalysis.topology.tpr.utils.</tt><tt class="descname">read_tpxheader</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#read_tpxheader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.read_tpxheader" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.topology.tpr.utils.</code><code class="descname">read_tpxheader</code><span class="sig-paren">(</span><em>data</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tpr/utils.html#read_tpxheader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.topology.tpr.utils.read_tpxheader" title="Permalink to this definition">¶</a></dt>
 <dd><p>this function is now compatible with do_tpxheader in tpxio.c</p>
 </dd></dl>
 
@@ -770,7 +762,7 @@ <h2>4.22.4. Utilities for the TPRParser<a class="headerlink" href="#utilities-fo
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -785,11 +777,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="tables.html" title="4.21. MDAnalysis topology tables"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../topology_modules.html" >4. Topology modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -799,7 +791,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology_modules.html b/package/doc/html/documentation_pages/topology_modules.html
index 6b68d83c02d..6dcf4533ca2 100644
--- a/package/doc/html/documentation_pages/topology_modules.html
+++ b/package/doc/html/documentation_pages/topology_modules.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>4. Topology modules &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>4. Topology modules &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="4.1. Topology readers — MDAnalysis.topology" href="topology/init.html" />
     <link rel="prev" title="3.6.2. Water dynamics analysis — MDAnalysis.analysis.waterdynamics" href="analysis/waterdynamics.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -50,26 +48,28 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="analysis/waterdynamics.html" title="3.6.2. Water dynamics analysis — MDAnalysis.analysis.waterdynamics"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../index.html">
               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h4>Previous topic</h4>
   <p class="topless"><a href="analysis/waterdynamics.html"
-                        title="previous chapter">3.6.2. Water dynamics analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></tt></a></p>
+                        title="previous chapter">3.6.2. Water dynamics analysis &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.analysis.waterdynamics</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="topology/init.html"
-                        title="next chapter">4.1. Topology readers &#8212; <tt class="docutils literal docutils literal"><span class="pre">MDAnalysis.topology</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/topology_modules.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">4.1. Topology readers &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/topology_modules.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -88,7 +88,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="topology-modules">
 <h1>4. Topology modules<a class="headerlink" href="#topology-modules" title="Permalink to this headline">¶</a></h1>
@@ -97,17 +97,17 @@ <h1>4. Topology modules<a class="headerlink" href="#topology-modules" title="Per
 between the atoms. It can use topology files from MD packages such as
 CHARMM&#8217;s and NAMD&#8217;s PSF format or Amber&#8217;s PRMTOP files. In addition,
 it can also glean atom information from single frame coordinate files
-such the PDB, CRD, or PQR formats (see the <a class="reference internal" href="topology/init.html#supported-topology-formats"><em>Table of Supported Topology Formats</em></a>).</p>
+such the PDB, CRD, or PQR formats (see the <a class="reference internal" href="topology/init.html#supported-topology-formats"><span>Table of Supported Topology Formats</span></a>).</p>
 <p>Typically, MDAnalysis recognizes formats by the file extension and
 hence most users probably do not need to concern themselves with
 classes and functions described here. However, if MDAnalysis does not
 properly recognize a file format then a user can explicitly set the
 topology file format in the <em>topology_format</em> keyword argument to
-<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><tt class="xref py py-class docutils literal"><span class="pre">Universe</span></tt></a>.</p>
+<a class="reference internal" href="core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe" title="MDAnalysis.core.AtomGroup.Universe"><code class="xref py py-class docutils literal"><span class="pre">Universe</span></code></a>.</p>
 <p class="rubric">Topology formats</p>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="topology/init.html">4.1. Topology readers &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.topology</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="topology/init.html">4.1. Topology readers &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/PSFParser.html">4.2. PSF topology parser</a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/TOPParser.html">4.3. AMBER PRMTOP topology parser</a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/CRDParser.html">4.4. CRD topology parser</a></li>
@@ -117,10 +117,10 @@ <h1>4. Topology modules<a class="headerlink" href="#topology-modules" title="Per
 <li class="toctree-l1"><a class="reference internal" href="topology/ExtendedPDBParser.html">4.8. Extended PDB topology parser</a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/PDBQTParser.html">4.9. PDBQT topology parser</a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/PQRParser.html">4.10. PQR topology parser</a></li>
-<li class="toctree-l1"><a class="reference internal" href="topology/DLPolyParser.html">4.11. DL Poly format Topology Readers &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="topology/DLPolyParser.html">4.11. DL Poly format Topology Readers &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology.DLPolyParser</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/DMSParser.html">4.12. DESRES Molecular Structure file format topology parser</a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/TPRParser.html">4.13. Gromacs portable run input TPR format parser</a></li>
-<li class="toctree-l1"><a class="reference internal" href="topology/MOL2Parser.html">4.14. MOL2 file format &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="topology/MOL2Parser.html">4.14. MOL2 file format &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.coordinates.MOL2</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/XYZParser.html">4.15. XYZ Topology Parser</a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/LAMMPSParser.html">4.16. LAMMPSParser</a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/GMSParser.html">4.17. GAMESS Topology Parser</a></li>
@@ -133,8 +133,8 @@ <h1>4. Topology modules<a class="headerlink" href="#topology-modules" title="Per
 the topology readers.</p>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="topology/base.html">4.19. Base topology reader classes &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.topology.base</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="topology/core.html">4.20. Common functions for topology building &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.topology.core</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="topology/base.html">4.19. Base topology reader classes &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology.base</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="topology/core.html">4.20. Common functions for topology building &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.topology.core</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/tables.html">4.21. MDAnalysis topology tables</a></li>
 <li class="toctree-l1"><a class="reference internal" href="topology/tpr_util.html">4.22. Utility functions for the TPR topology parser</a></li>
 </ul>
@@ -147,7 +147,7 @@ <h1>4. Topology modules<a class="headerlink" href="#topology-modules" title="Per
       </div>
       <div class="clearer"></div>
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+    <div class="related" role="navigation" aria-label="related navigation">
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@@ -162,10 +162,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="analysis/waterdynamics.html" title="3.6.2. Water dynamics analysis — MDAnalysis.analysis.waterdynamics"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
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-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
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@@ -175,7 +175,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/units.html b/package/doc/html/documentation_pages/units.html
index b58641213e1..a8914e16eb6 100644
--- a/package/doc/html/documentation_pages/units.html
+++ b/package/doc/html/documentation_pages/units.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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@@ -8,7 +6,7 @@
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-    <title>11. Constants and unit conversion — MDAnalysis.units &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>11. Constants and unit conversion — MDAnalysis.units &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
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+        VERSION:     '0.11.0',
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         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
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+          title="Search within MDAnalysis 0.11.0 documentation"
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     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="12. Custom exceptions and warnings — MDAnalysis.exceptions" href="exceptions.html" />
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+    <div class="related" role="navigation" aria-label="related navigation">
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              accesskey="N">next</a> |</li>
         <li class="right" >
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+          <a href="version.html" title="10. Version information for MDAnalysis — MDAnalysis.version"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
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   <h3><a href="../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">11. Constants and unit conversion &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.units</span></tt></a><ul>
+<li><a class="reference internal" href="#">11. Constants and unit conversion &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.units</span></code></a><ul>
 <li><a class="reference internal" href="#implementation-notes">11.1. Implementation notes</a><ul>
 <li><a class="reference internal" href="#conversions">11.1.1. Conversions</a></li>
 </ul>
@@ -74,16 +72,18 @@ <h3><a href="../index.html">Table Of Contents</a></h3>
 
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   <h4>Next topic</h4>
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-  <h3>This Page</h3>
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-    <li><a href="../_sources/documentation_pages/units.txt"
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-  </ul>
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+                        title="next chapter">12. Custom exceptions and warnings &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.exceptions</span></code></a></p>
+  <div role="note" aria-label="source link">
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@@ -102,10 +102,10 @@ <h3>Quick search</h3>
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   <span class="target" id="module-MDAnalysis.units"></span><div class="section" id="constants-and-unit-conversion-mdanalysis-units">
-<h1>11. Constants and unit conversion &#8212; <a class="reference internal" href="#module-MDAnalysis.units" title="MDAnalysis.units"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.units</span></tt></a><a class="headerlink" href="#constants-and-unit-conversion-mdanalysis-units" title="Permalink to this headline">¶</a></h1>
+<h1>11. Constants and unit conversion &#8212; <a class="reference internal" href="#module-MDAnalysis.units" title="MDAnalysis.units"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.units</span></code></a><a class="headerlink" href="#constants-and-unit-conversion-mdanalysis-units" title="Permalink to this headline">¶</a></h1>
 <p>The base units of MDAnalysis trajectories are the <strong>Å</strong> (<strong>ångström</strong>) for
 <strong>length</strong> and <strong>ps</strong> (<strong>pico second</strong>) for <strong>time</strong>. By default, all positions
 are in Å and all times are in ps, regardless of how the MD code stored
@@ -113,9 +113,9 @@ <h1>11. Constants and unit conversion &#8212; <a class="reference internal" href
 MDAnalysis units when reading trajectories and converts back when writing. This
 makes it possible to write scripts that can be agnostic of the specifics of how
 a particular MD code stores trajectory data. Other base units are listed in the
-table on <a class="reference internal" href="#table-baseunits"><em>Base units in MDAnalysis</em></a>.</p>
-<table border="1" class="docutils" id="table-baseunits">
-<caption>Base units in MDAnalysis</caption>
+table on <a class="reference internal" href="#table-baseunits"><span>Base units in MDAnalysis</span></a>.</p>
+<table border="1" class="docutils" id="id4">
+<span id="table-baseunits"></span><caption><span class="caption-text">Base units in MDAnalysis</span><a class="headerlink" href="#id4" title="Permalink to this table">¶</a></caption>
 <colgroup>
 <col width="15%" />
 <col width="19%" />
@@ -156,9 +156,9 @@ <h1>11. Constants and unit conversion &#8212; <a class="reference internal" href
 </table>
 <div class="section" id="implementation-notes">
 <h2>11.1. Implementation notes<a class="headerlink" href="#implementation-notes" title="Permalink to this headline">¶</a></h2>
-<p>All conversions with <a class="reference internal" href="#MDAnalysis.units.convert" title="MDAnalysis.units.convert"><tt class="xref py py-func docutils literal"><span class="pre">convert()</span></tt></a> are carried out in a simple fashion: the
+<p>All conversions with <a class="reference internal" href="#MDAnalysis.units.convert" title="MDAnalysis.units.convert"><code class="xref py py-func docutils literal"><span class="pre">convert()</span></code></a> are carried out in a simple fashion: the
 conversion factor <span class="math">\(f_{b,b'}\)</span> from the base unit <span class="math">\(b\)</span> to another unit
-<span class="math">\(b'\)</span> is precomputed and stored (see <a class="reference internal" href="#data"><em>Data</em></a>). The numerical value of
+<span class="math">\(b'\)</span> is precomputed and stored (see <a class="reference internal" href="#data"><span>Data</span></a>). The numerical value of
 a quantity in unit <span class="math">\(b\)</span> is <span class="math">\(X/b\)</span> (e.g. for <span class="math">\(X =
 1.23\,\mathrm{ps}\)</span> the numerical value is <span class="math">\(X/\mathrm{ps} =
 1.23\)</span>). <a class="footnote-reference" href="#funits" id="id1">[1]</a></p>
@@ -166,18 +166,19 @@ <h2>11.1. Implementation notes<a class="headerlink" href="#implementation-notes"
 is then</p>
 <div class="math">
 \[X'/b' = f_{b,b'} X/b\]</div>
-<p>The function <a class="reference internal" href="#MDAnalysis.units.get_conversion_factor" title="MDAnalysis.units.get_conversion_factor"><tt class="xref py py-func docutils literal"><span class="pre">get_conversion_factor()</span></tt></a> returns the appropriate factor
+<p>The function <a class="reference internal" href="#MDAnalysis.units.get_conversion_factor" title="MDAnalysis.units.get_conversion_factor"><code class="xref py py-func docutils literal"><span class="pre">get_conversion_factor()</span></code></a> returns the appropriate factor
 <span class="math">\(f_{b,b'}\)</span>.</p>
 <p>Conversion between different units is always carried out via the base unit as
 an intermediate step:</p>
-<div class="highlight-python"><pre>x is in u1: from u1 to b:  x'  = x  / factor[u1]
-            from b  to u2: x'' = x' * factor[u2]
-so f[u1,u2] = factor[u2]/factor[u1]</pre>
+<div class="highlight-python"><div class="highlight"><pre>x is in u1: from u1 to b:  x&#39;  = x  / factor[u1]
+            from b  to u2: x&#39;&#39; = x&#39; * factor[u2]
+so f[u1,u2] = factor[u2]/factor[u1]
+</pre></div>
 </div>
 <div class="section" id="conversions">
 <h3>11.1.1. Conversions<a class="headerlink" href="#conversions" title="Permalink to this headline">¶</a></h3>
 <p>Examples for how to calculate some of the conversion factors that are
-hard-coded in <a class="reference internal" href="#module-MDAnalysis.units" title="MDAnalysis.units"><tt class="xref py py-mod docutils literal"><span class="pre">units</span></tt></a> (see <a class="reference internal" href="#data"><em>Data</em></a>).</p>
+hard-coded in <a class="reference internal" href="#module-MDAnalysis.units" title="MDAnalysis.units"><code class="xref py py-mod docutils literal"><span class="pre">units</span></code></a> (see <a class="reference internal" href="#data"><span>Data</span></a>).</p>
 <dl class="docutils">
 <dt>density:</dt>
 <dd><p class="first">Base unit is <span class="math">\(\mathrm{Å}^{-3}\)</span>:</p>
@@ -195,19 +196,21 @@ <h3>11.1.1. Conversions<a class="headerlink" href="#conversions" title="Permalin
 </dd>
 <dt>concentration:</dt>
 <dd><p class="first">Example for how to convert the conversion factor to Molar (mol/l):</p>
-<div class="highlight-python"><pre>factor = 1 A**-3 / (N_Avogadro * (10**-9 dm)**-3)</pre>
+<div class="highlight-python"><div class="highlight"><pre>factor = 1 A**-3 / (N_Avogadro * (10**-9 dm)**-3)
+</pre></div>
 </div>
 <p>relative to a density rho0 in g/cm^3:</p>
-<div class="highlight-python"><pre>M(H2O) = 18 g/mol   Molar mass of water
+<div class="highlight-python"><div class="highlight"><pre>M(H2O) = 18 g/mol   Molar mass of water
 
-factor = 1/(1e-24 * N_Avogadro / M(H2O))</pre>
+factor = 1/(1e-24 * N_Avogadro / M(H2O))
+</pre></div>
 </div>
 <p class="last">from <cite>rho/rho0 = n/(N_A * M**-1) / rho0</cite>  where <cite>[n] = 1/Volume</cite>, <cite>[rho] = mass/Volume</cite></p>
 </dd>
 </dl>
-<div class="admonition-see-also admonition seealso">
+<div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<p class="last">Maybe we should simply use <a class="reference external" href="http://packages.python.org/quantities/">Quantities</a> or <a class="reference external" href="http://docs.scipy.org/doc/scipy/reference/constants.html#module-scipy.constants" title="(in SciPy v0.16.0)"><tt class="xref py py-mod docutils literal"><span class="pre">scipy.constants</span></tt></a>?</p>
+<p class="last">Maybe we should simply use <a class="reference external" href="http://packages.python.org/quantities/">Quantities</a> or <a class="reference external" href="http://docs.scipy.org/doc/scipy/reference/constants.html#module-scipy.constants" title="(in SciPy v0.16.0)"><code class="xref py py-mod docutils literal"><span class="pre">scipy.constants</span></code></a>?</p>
 </div>
 </div>
 </div>
@@ -215,7 +218,7 @@ <h3>11.1.1. Conversions<a class="headerlink" href="#conversions" title="Permalin
 <h2>11.2. Functions<a class="headerlink" href="#functions" title="Permalink to this headline">¶</a></h2>
 <dl class="function">
 <dt id="MDAnalysis.units.get_conversion_factor">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">get_conversion_factor</tt><big>(</big><em>unit_type</em>, <em>u1</em>, <em>u2</em><big>)</big><a class="reference internal" href="../_modules/MDAnalysis/units.html#get_conversion_factor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.units.get_conversion_factor" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">get_conversion_factor</code><span class="sig-paren">(</span><em>unit_type</em>, <em>u1</em>, <em>u2</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/MDAnalysis/units.html#get_conversion_factor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.units.get_conversion_factor" title="Permalink to this definition">¶</a></dt>
 <dd><p>generate the conversion factor u1 -&gt; u2 by using the base unit as an intermediate</p>
 <p>f[u1 -&gt; u2] = factor[u2]/factor[u1]</p>
 <p>Conversion of X (in u1) to X&#8217; (in u2):</p>
@@ -225,15 +228,15 @@ <h2>11.2. Functions<a class="headerlink" href="#functions" title="Permalink to t
 
 <dl class="function">
 <dt id="MDAnalysis.units.convert">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">convert</tt><big>(</big><em>x</em>, <em>u1</em>, <em>u2</em><big>)</big><a class="reference internal" href="../_modules/MDAnalysis/units.html#convert"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.units.convert" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">convert</code><span class="sig-paren">(</span><em>x</em>, <em>u1</em>, <em>u2</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/MDAnalysis/units.html#convert"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.units.convert" title="Permalink to this definition">¶</a></dt>
 <dd><p>Convert value <em>x</em> in unit <em>u1</em> to new value in <em>u2</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">Converted value.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Converted value.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body"><tt class="xref py py-exc docutils literal"><span class="pre">ValueError</span></tt> if the units are not known or if
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> if the units are not known or if
 one attempts to convert between incompatible
 units.</td>
 </tr>
@@ -246,17 +249,18 @@ <h2>11.2. Functions<a class="headerlink" href="#functions" title="Permalink to t
 <span id="id2"></span><h2>11.3. Data<a class="headerlink" href="#data" title="Permalink to this headline">¶</a></h2>
 <dl class="data">
 <dt id="MDAnalysis.units.constants">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">constants</tt><em class="property"> = {u'elementary_charge': 1.602176565e-19, u'N_Avogadro': 6.02214129e+23, u'calorie': 4.184}</em><a class="headerlink" href="#MDAnalysis.units.constants" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">constants</code><em class="property"> = {u'elementary_charge': 1.602176565e-19, u'N_Avogadro': 6.02214129e+23, u'calorie': 4.184}</em><a class="headerlink" href="#MDAnalysis.units.constants" title="Permalink to this definition">¶</a></dt>
 <dd><p>Values of physical constants are taken from <a class="reference external" href="http://physics.nist.gov/cuu/Constants/">CODATA 2010 at NIST</a>. The
 thermochemical calorie is defined in the <a class="reference external" href="http://www.iso.org/iso/catalogue_detail?csnumber=31890">ISO 80000-5:2007</a> standard
 and is also listed in the <a class="reference external" href="http://physics.nist.gov/Pubs/SP811/appenB8.html#C">NIST Guide to SI: Appendix B.8: Factors for Units</a>.</p>
-<p class="versionadded">
-<span class="versionmodified">New in version 0.9.0.</span></p>
+<div class="versionadded">
+<p><span class="versionmodified">New in version 0.9.0.</span></p>
+</div>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.units.lengthUnit_factor">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">lengthUnit_factor</tt><em class="property"> = {u'A': 1.0, '\xe2\x84\xab': 1.0, u'Angstrom': 1.0, u'nanometer': 0.1, u'fm': 100000.0, u'nm': 0.1, u'\u212b': 1.0, u'angstrom': 1.0, u'femtometer': 100000.0, u'pm': 100.0, u'picometer': 100.0}</em><a class="headerlink" href="#MDAnalysis.units.lengthUnit_factor" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">lengthUnit_factor</code><em class="property"> = {u'A': 1.0, '\xe2\x84\xab': 1.0, u'Angstrom': 1.0, u'nanometer': 0.1, u'fm': 100000.0, u'nm': 0.1, u'\u212b': 1.0, u'angstrom': 1.0, u'femtometer': 100000.0, u'pm': 100.0, u'picometer': 100.0}</em><a class="headerlink" href="#MDAnalysis.units.lengthUnit_factor" title="Permalink to this definition">¶</a></dt>
 <dd><p>The basic unit of <em>length</em> in MDAnalysis is the Angstrom.
 Conversion factors between the base unit and other lengthUnits <em>x</em> are stored.
 Conversions follow <cite>L/x = L/Angstrom * lengthUnit_factor[x]</cite>.
@@ -265,20 +269,22 @@ <h2>11.2. Functions<a class="headerlink" href="#functions" title="Permalink to t
 
 <dl class="data">
 <dt id="MDAnalysis.units.N_Avogadro">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">N_Avogadro</tt><em class="property"> = 6.02214129e+23</em><a class="headerlink" href="#MDAnalysis.units.N_Avogadro" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">N_Avogadro</code><em class="property"> = 6.02214129e+23</em><a class="headerlink" href="#MDAnalysis.units.N_Avogadro" title="Permalink to this definition">¶</a></dt>
 <dd><p><a class="reference external" href="http://physics.nist.gov/cgi-bin/cuu/Value?na">Avogadro&#8217;s constant</a> in mol**-1.</p>
-<p class="deprecated">
-<span class="versionmodified">Deprecated since version 0.9.0: </span>Use <em>N_Avogadro</em> in dict <a class="reference internal" href="#MDAnalysis.units.constants" title="MDAnalysis.units.constants"><tt class="xref py py-data docutils literal"><span class="pre">constants</span></tt></a> instead.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Use CODATA 2010 value, which differs from the previously used value
+<div class="deprecated">
+<p><span class="versionmodified">Deprecated since version 0.9.0: </span>Use <em>N_Avogadro</em> in dict <a class="reference internal" href="#MDAnalysis.units.constants" title="MDAnalysis.units.constants"><code class="xref py py-data docutils literal"><span class="pre">constants</span></code></a> instead.</p>
+</div>
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Use CODATA 2010 value, which differs from the previously used value
 6.02214179e+23 mol**-1 by -5.00000000e+16 mol**-1.</p>
+</div>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.units.water">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">water</tt><em class="property"> = {u'MolarMass': 18.016, u'SPC': 0.985, u'TIP4P': 1.001, u'exp': 0.997, u'TIP3P': 1.002}</em><a class="headerlink" href="#MDAnalysis.units.water" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">water</code><em class="property"> = {u'MolarMass': 18.016, u'SPC': 0.985, u'TIP4P': 1.001, u'exp': 0.997, u'TIP3P': 1.002}</em><a class="headerlink" href="#MDAnalysis.units.water" title="Permalink to this definition">¶</a></dt>
 <dd><dl class="docutils">
-<dt>water density values at T=298K, P=1atm <a class="reference internal" href="#jorgensen1998">[Jorgensen1998]</a></dt>
+<dt>water density values at T=298K, P=1atm <a class="reference internal" href="#jorgensen1998" id="id3">[Jorgensen1998]</a></dt>
 <dd><table border="1" class="first last docutils">
 <colgroup>
 <col width="47%" />
@@ -311,54 +317,55 @@ <h2>11.2. Functions<a class="headerlink" href="#functions" title="Permalink to t
 
 <dl class="data">
 <dt id="MDAnalysis.units.densityUnit_factor">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">densityUnit_factor</tt><em class="property"> = {u'Molar': 1660.5389210321898, u'Angstrom^{-3}': 1.0, u'TIP3P': 29.85655608913766, u'water': 30.00628806551247, u'nm^{-3}': 1000.0, '\xe2\x84\xab^{-3}': 1.0, u'TIP4P': 29.886382818497438, u'A^{-3}': 1.0, u'nanometer^{-3}': 1000.0, u'\u212b^{-3}': 1.0, u'SPC': 30.37184690488927}</em><a class="headerlink" href="#MDAnalysis.units.densityUnit_factor" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">densityUnit_factor</code><em class="property"> = {u'Molar': 1660.5389210321898, u'Angstrom^{-3}': 1.0, u'TIP3P': 29.85655608913766, u'water': 30.00628806551247, u'nm^{-3}': 1000.0, '\xe2\x84\xab^{-3}': 1.0, u'TIP4P': 29.886382818497438, u'A^{-3}': 1.0, u'nanometer^{-3}': 1000.0, u'\u212b^{-3}': 1.0, u'SPC': 30.37184690488927}</em><a class="headerlink" href="#MDAnalysis.units.densityUnit_factor" title="Permalink to this definition">¶</a></dt>
 <dd><p>The basic unit for <em>densities</em> is Angstroem**(-3), i.e.
 the volume per molecule in A**3. Especially for water
 it can be convenient to measure the density relative to bulk, and
-hence a number of values are pre-stored in <a class="reference internal" href="#MDAnalysis.units.water" title="MDAnalysis.units.water"><tt class="xref py py-data docutils literal"><span class="pre">water</span></tt></a>.</p>
+hence a number of values are pre-stored in <a class="reference internal" href="#MDAnalysis.units.water" title="MDAnalysis.units.water"><code class="xref py py-data docutils literal"><span class="pre">water</span></code></a>.</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.units.timeUnit_factor">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">timeUnit_factor</tt><em class="property"> = {u'ps': 1.0, u'second': 1e-12, u'fs': 1000.0, u'sec': 1e-12, u'picosecond': 1.0, u'femtosecond': 1000.0, u'AKMA': 20.45482949774598, u'ns': 0.001, u'nanosecond': 0.001, u's': 1e-12}</em><a class="headerlink" href="#MDAnalysis.units.timeUnit_factor" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">timeUnit_factor</code><em class="property"> = {u'ps': 1.0, u'second': 1e-12, u'fs': 1000.0, u'sec': 1e-12, u'picosecond': 1.0, u'femtosecond': 1000.0, u'AKMA': 20.45482949774598, u'ns': 0.001, u'nanosecond': 0.001, u's': 1e-12}</em><a class="headerlink" href="#MDAnalysis.units.timeUnit_factor" title="Permalink to this definition">¶</a></dt>
 <dd><p>For <em>time</em>, the basic unit is ps; in particular CHARMM&#8217;s
 1 <a class="reference external" href="http://www.charmm.org/documentation/c37b1/usage.html#%20AKMA">AKMA</a> time unit = 4.888821E-14 sec is supported.</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.units.speedUnit_factor">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">speedUnit_factor</tt><em class="property"> = {u'Angstrom/picosecond': 1.0, u'm/s': 100.0, u'nm/ps': 0.1, '\xe2\x84\xab/ps': 1.0, u'nm/ns': 100.0, u'\u212b/ps': 1.0, u'Angstrom/AKMA': 0.04888821, u'pm/ps': 100.0, u'angstrom/picosecond': 1.0, u'A/ps': 1.0, u'Angstrom/ps': 1.0, u'nanometer/picosecond': 0.1, u'nanometer/ps': 0.1}</em><a class="headerlink" href="#MDAnalysis.units.speedUnit_factor" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">speedUnit_factor</code><em class="property"> = {u'Angstrom/picosecond': 1.0, u'm/s': 100.0, u'nm/ps': 0.1, '\xe2\x84\xab/ps': 1.0, u'nm/ns': 100.0, u'\u212b/ps': 1.0, u'Angstrom/AKMA': 0.04888821, u'pm/ps': 100.0, u'angstrom/picosecond': 1.0, u'A/ps': 1.0, u'Angstrom/ps': 1.0, u'nanometer/picosecond': 0.1, u'nanometer/ps': 0.1}</em><a class="headerlink" href="#MDAnalysis.units.speedUnit_factor" title="Permalink to this definition">¶</a></dt>
 <dd><p>For <em>speed</em>, the basic unit is Angstrom/ps.</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.units.forceUnit_factor">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">forceUnit_factor</tt><em class="property"> = {u'N': 1.66053892103219e-11, u'kcal/(mol*Angstrom)': 0.2390057361376673, u'kJ/(mol*Angstrom)': 1.0, u'kJ/(mol*A)': 1.0, u'kJ/(mol*\u212b)': 1.0, u'Newton': 1.66053892103219e-11, 'kJ/(mol*\xe2\x84\xab)': 1.0, u'J/m': 1.66053892103219e-11, u'kJ/(mol*nm)': 10.0}</em><a class="headerlink" href="#MDAnalysis.units.forceUnit_factor" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">forceUnit_factor</code><em class="property"> = {u'N': 1.66053892103219e-11, u'kcal/(mol*Angstrom)': 0.2390057361376673, u'kJ/(mol*Angstrom)': 1.0, u'kJ/(mol*A)': 1.0, u'kJ/(mol*\u212b)': 1.0, u'Newton': 1.66053892103219e-11, 'kJ/(mol*\xe2\x84\xab)': 1.0, u'J/m': 1.66053892103219e-11, u'kJ/(mol*nm)': 10.0}</em><a class="headerlink" href="#MDAnalysis.units.forceUnit_factor" title="Permalink to this definition">¶</a></dt>
 <dd><p>For <em>force</em> the basic unit is kJ/(mol*Angstrom).</p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.units.chargeUnit_factor">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">chargeUnit_factor</tt><em class="property"> = {u'Amber': 18.2223, u'C': 1.602176565e-19, u'e': 1.0, u'As': 1.602176565e-19}</em><a class="headerlink" href="#MDAnalysis.units.chargeUnit_factor" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">chargeUnit_factor</code><em class="property"> = {u'Amber': 18.2223, u'C': 1.602176565e-19, u'e': 1.0, u'As': 1.602176565e-19}</em><a class="headerlink" href="#MDAnalysis.units.chargeUnit_factor" title="Permalink to this definition">¶</a></dt>
 <dd><p><em>Charge</em> is measured in multiples of the <a class="reference external" href="http://physics.nist.gov/cgi-bin/cuu/Value?e">electron charge</a> <em>e</em>, with the value
-<em>elementary_charge</em> in <a class="reference internal" href="#MDAnalysis.units.constants" title="MDAnalysis.units.constants"><tt class="xref py py-data docutils literal"><span class="pre">constants</span></tt></a>.
+<em>elementary_charge</em> in <a class="reference internal" href="#MDAnalysis.units.constants" title="MDAnalysis.units.constants"><code class="xref py py-data docutils literal"><span class="pre">constants</span></code></a>.
 The <a class="reference external" href="http://ambermd.org/formats.html#parm">conversion factor to Amber charge units</a> is 18.2223.</p>
-<p class="versionchanged">
-<span class="versionmodified">Changed in version 0.9.0: </span>Use CODATA 2010 value for <em>elementary charge</em>, which differs from the previously used value
+<div class="versionchanged">
+<p><span class="versionmodified">Changed in version 0.9.0: </span>Use CODATA 2010 value for <em>elementary charge</em>, which differs from the previously used value
 <em>e</em> =  1.602176487 x 10**(-19) C by 7.8000000e-27 C.</p>
+</div>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.units.conversion_factor">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">conversion_factor</tt><em class="property"> = {u'force': {u'N': 1.66053892103219e-11, u'kcal/(mol*Angstrom)': 0.2390057361376673, u'kJ/(mol*Angstrom)': 1.0, u'kJ/(mol*A)': 1.0, u'kJ/(mol*\u212b)': 1.0, u'Newton': 1.66053892103219e-11, 'kJ/(mol*\xe2\x84\xab)': 1.0, u'J/m': 1.66053892103219e-11, u'kJ/(mol*nm)': 10.0}, u'density': {u'Molar': 1660.5389210321898, u'Angstrom^{-3}': 1.0, u'TIP3P': 29.85655608913766, u'water': 30.00628806551247, u'nm^{-3}': 1000.0, '\xe2\x84\xab^{-3}': 1.0, u'TIP4P': 29.886382818497438, u'A^{-3}': 1.0, u'nanometer^{-3}': 1000.0, u'\u212b^{-3}': 1.0, u'SPC': 30.37184690488927}, u'energy': {u'kcal/mol': 0.2390057361376673, u'J': 1.66053892103219e-21, u'kJ/mol': 1.0, u'eV': 0.01036426919046959}, u'charge': {u'Amber': 18.2223, u'C': 1.602176565e-19, u'e': 1.0, u'As': 1.602176565e-19}, u'length': {u'A': 1.0, '\xe2\x84\xab': 1.0, u'Angstrom': 1.0, u'nanometer': 0.1, u'fm': 100000.0, u'nm': 0.1, u'\u212b': 1.0, u'angstrom': 1.0, u'femtometer': 100000.0, u'pm': 100.0, u'picometer': 100.0}, u'time': {u'ps': 1.0, u'second': 1e-12, u'fs': 1000.0, u'sec': 1e-12, u'picosecond': 1.0, u'femtosecond': 1000.0, u'AKMA': 20.45482949774598, u'ns': 0.001, u'nanosecond': 0.001, u's': 1e-12}, u'speed': {u'Angstrom/picosecond': 1.0, u'm/s': 100.0, u'nm/ps': 0.1, '\xe2\x84\xab/ps': 1.0, u'nm/ns': 100.0, u'\u212b/ps': 1.0, u'Angstrom/AKMA': 0.04888821, u'pm/ps': 100.0, u'angstrom/picosecond': 1.0, u'A/ps': 1.0, u'Angstrom/ps': 1.0, u'nanometer/picosecond': 0.1, u'nanometer/ps': 0.1}}</em><a class="headerlink" href="#MDAnalysis.units.conversion_factor" title="Permalink to this definition">¶</a></dt>
-<dd><p><a class="reference internal" href="#MDAnalysis.units.conversion_factor" title="MDAnalysis.units.conversion_factor"><tt class="xref py py-data docutils literal"><span class="pre">conversion_factor</span></tt></a> is used by <a class="reference internal" href="#MDAnalysis.units.get_conversion_factor" title="MDAnalysis.units.get_conversion_factor"><tt class="xref py py-func docutils literal"><span class="pre">get_conversion_factor()</span></tt></a>:
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">conversion_factor</code><em class="property"> = {u'force': {u'N': 1.66053892103219e-11, u'kcal/(mol*Angstrom)': 0.2390057361376673, u'kJ/(mol*Angstrom)': 1.0, u'kJ/(mol*A)': 1.0, u'kJ/(mol*\u212b)': 1.0, u'Newton': 1.66053892103219e-11, 'kJ/(mol*\xe2\x84\xab)': 1.0, u'J/m': 1.66053892103219e-11, u'kJ/(mol*nm)': 10.0}, u'density': {u'Molar': 1660.5389210321898, u'Angstrom^{-3}': 1.0, u'TIP3P': 29.85655608913766, u'water': 30.00628806551247, u'nm^{-3}': 1000.0, '\xe2\x84\xab^{-3}': 1.0, u'TIP4P': 29.886382818497438, u'A^{-3}': 1.0, u'nanometer^{-3}': 1000.0, u'\u212b^{-3}': 1.0, u'SPC': 30.37184690488927}, u'energy': {u'kcal/mol': 0.2390057361376673, u'J': 1.66053892103219e-21, u'kJ/mol': 1.0, u'eV': 0.01036426919046959}, u'charge': {u'Amber': 18.2223, u'C': 1.602176565e-19, u'e': 1.0, u'As': 1.602176565e-19}, u'length': {u'A': 1.0, '\xe2\x84\xab': 1.0, u'Angstrom': 1.0, u'nanometer': 0.1, u'fm': 100000.0, u'nm': 0.1, u'\u212b': 1.0, u'angstrom': 1.0, u'femtometer': 100000.0, u'pm': 100.0, u'picometer': 100.0}, u'time': {u'ps': 1.0, u'second': 1e-12, u'fs': 1000.0, u'sec': 1e-12, u'picosecond': 1.0, u'femtosecond': 1000.0, u'AKMA': 20.45482949774598, u'ns': 0.001, u'nanosecond': 0.001, u's': 1e-12}, u'speed': {u'Angstrom/picosecond': 1.0, u'm/s': 100.0, u'nm/ps': 0.1, '\xe2\x84\xab/ps': 1.0, u'nm/ns': 100.0, u'\u212b/ps': 1.0, u'Angstrom/AKMA': 0.04888821, u'pm/ps': 100.0, u'angstrom/picosecond': 1.0, u'A/ps': 1.0, u'Angstrom/ps': 1.0, u'nanometer/picosecond': 0.1, u'nanometer/ps': 0.1}}</em><a class="headerlink" href="#MDAnalysis.units.conversion_factor" title="Permalink to this definition">¶</a></dt>
+<dd><p><a class="reference internal" href="#MDAnalysis.units.conversion_factor" title="MDAnalysis.units.conversion_factor"><code class="xref py py-data docutils literal"><span class="pre">conversion_factor</span></code></a> is used by <a class="reference internal" href="#MDAnalysis.units.get_conversion_factor" title="MDAnalysis.units.get_conversion_factor"><code class="xref py py-func docutils literal"><span class="pre">get_conversion_factor()</span></code></a>:
 Note: any observable with a unit (i.e. one with an entry in
-the <tt class="xref py py-attr docutils literal"><span class="pre">unit</span></tt> attribute) needs an entry in <a class="reference internal" href="#MDAnalysis.units.conversion_factor" title="MDAnalysis.units.conversion_factor"><tt class="xref py py-data docutils literal"><span class="pre">conversion_factor</span></tt></a></p>
+the <code class="xref py py-attr docutils literal"><span class="pre">unit</span></code> attribute) needs an entry in <a class="reference internal" href="#MDAnalysis.units.conversion_factor" title="MDAnalysis.units.conversion_factor"><code class="xref py py-data docutils literal"><span class="pre">conversion_factor</span></code></a></p>
 </dd></dl>
 
 <dl class="data">
 <dt id="MDAnalysis.units.unit_types">
-<tt class="descclassname">MDAnalysis.units.</tt><tt class="descname">unit_types</tt><em class="property"> = {u'kcal/mol': u'energy', u'kJ/mol': u'energy', u'm/s': u'speed', u'kJ/(mol*\u212b)': u'force', u'Angstrom^{-3}': u'density', u'pm/ps': u'speed', u'second': u'time', u'A': u'length', u'Angstrom': u'length', u'nm/ns': u'speed', u'\u212b/ps': u'speed', u'Angstrom/picosecond': u'speed', u'Angstrom/AKMA': u'speed', u'nanometer': u'length', u'TIP4P': u'density', u'ps': u'time', u'kcal/(mol*Angstrom)': u'force', u'angstrom/picosecond': u'speed', u'nm': u'length', u'nanometer^{-3}': u'density', u'\u212b': u'length', u'A/ps': u'speed', u'nanosecond': u'time', u'ns': u'time', u'angstrom': u'length', u'kJ/(mol*A)': u'force', u'AKMA': u'time', u'SPC': u'density', u'pm': u'length', u'Molar': u'density', u'C': u'charge', u'fs': u'time', u'eV': u'energy', u'femtosecond': u'time', u's': u'time', u'J': u'energy', u'nm/ps': u'speed', '\xe2\x84\xab/ps': u'speed', '\xe2\x84\xab': u'length', u'N': u'force', u'water': u'density', u'nanometer/ps': u'speed', u'nm^{-3}': u'density', u'picosecond': u'time', '\xe2\x84\xab^{-3}': u'density', u'TIP3P': u'density', u'fm': u'length', u'Amber': u'charge', u'A^{-3}': u'density', u'e': u'charge', u'nanometer/picosecond': u'speed', 'kJ/(mol*\xe2\x84\xab)': u'force', u'Newton': u'force', u'Angstrom/ps': u'speed', u'\u212b^{-3}': u'density', u'As': u'charge', u'kJ/(mol*Angstrom)': u'force', u'femtometer': u'length', u'sec': u'time', u'picometer': u'length', u'J/m': u'force', u'kJ/(mol*nm)': u'force'}</em><a class="headerlink" href="#MDAnalysis.units.unit_types" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.units.</code><code class="descname">unit_types</code><em class="property"> = {u'kcal/mol': u'energy', u'kJ/mol': u'energy', u'm/s': u'speed', u'kJ/(mol*\u212b)': u'force', u'Angstrom^{-3}': u'density', u'pm/ps': u'speed', u'second': u'time', u'A': u'length', u'Angstrom': u'length', u'nm/ns': u'speed', u'\u212b/ps': u'speed', u'Angstrom/picosecond': u'speed', u'Angstrom/AKMA': u'speed', u'nanometer': u'length', u'TIP4P': u'density', u'ps': u'time', u'kcal/(mol*Angstrom)': u'force', u'angstrom/picosecond': u'speed', u'nm': u'length', u'nanometer^{-3}': u'density', u'\u212b': u'length', u'A/ps': u'speed', u'nanosecond': u'time', u'ns': u'time', u'angstrom': u'length', u'kJ/(mol*A)': u'force', u'AKMA': u'time', u'SPC': u'density', u'pm': u'length', u'Molar': u'density', u'C': u'charge', u'fs': u'time', u'eV': u'energy', u'femtosecond': u'time', u's': u'time', u'J': u'energy', u'nm/ps': u'speed', '\xe2\x84\xab/ps': u'speed', '\xe2\x84\xab': u'length', u'N': u'force', u'water': u'density', u'nanometer/ps': u'speed', u'nm^{-3}': u'density', u'picosecond': u'time', '\xe2\x84\xab^{-3}': u'density', u'TIP3P': u'density', u'fm': u'length', u'Amber': u'charge', u'A^{-3}': u'density', u'e': u'charge', u'nanometer/picosecond': u'speed', 'kJ/(mol*\xe2\x84\xab)': u'force', u'Newton': u'force', u'Angstrom/ps': u'speed', u'\u212b^{-3}': u'density', u'As': u'charge', u'kJ/(mol*Angstrom)': u'force', u'femtometer': u'length', u'sec': u'time', u'picometer': u'length', u'J/m': u'force', u'kJ/(mol*nm)': u'force'}</em><a class="headerlink" href="#MDAnalysis.units.unit_types" title="Permalink to this definition">¶</a></dt>
 <dd><p>Generated lookup table (dict): returns the type of unit for a known input unit.
 Note: Any unit must be <em>unique</em> because this dict is used to guess the
 unit type.</p>
@@ -397,7 +404,7 @@ <h2>11.4. References and footnotes<a class="headerlink" href="#references-and-fo
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -410,12 +417,12 @@ <h3>Navigation</h3>
           <a href="exceptions.html" title="12. Custom exceptions and warnings — MDAnalysis.exceptions"
              >next</a> |</li>
         <li class="right" >
-          <a href="version.html" title="10. Version information for MDAnalysis"
+          <a href="version.html" title="10. Version information for MDAnalysis — MDAnalysis.version"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -425,7 +432,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/version.html b/package/doc/html/documentation_pages/version.html
index 6d2bc2e3abf..8d2e492ef36 100644
--- a/package/doc/html/documentation_pages/version.html
+++ b/package/doc/html/documentation_pages/version.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>10. Version information for MDAnalysis — MDAnalysis.version &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>10. Version information for MDAnalysis — MDAnalysis.version &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="11. Constants and unit conversion — MDAnalysis.units" href="units.html" />
     <link rel="prev" title="9.9. Helper functions — MDAnalysis.lib.util" href="lib/util.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -50,17 +48,17 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="lib/util.html" title="9.9. Helper functions — MDAnalysis.lib.util"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../index.html">
               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
   <h3><a href="../index.html">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">10. Version information for MDAnalysis — <tt class="docutils literal"><span class="pre">MDAnalysis.version</span></tt></a><ul>
+<li><a class="reference internal" href="#">10. Version information for MDAnalysis — <code class="docutils literal"><span class="pre">MDAnalysis.version</span></code></a><ul>
 <li><a class="reference internal" href="#data">10.1. Data</a></li>
 </ul>
 </li>
@@ -68,16 +66,18 @@ <h3><a href="../index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="lib/util.html"
-                        title="previous chapter">9.9. Helper functions &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.lib.util</span></tt></a></p>
+                        title="previous chapter">9.9. Helper functions &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.lib.util</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="units.html"
-                        title="next chapter">11. Constants and unit conversion &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.units</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/version.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+                        title="next chapter">11. Constants and unit conversion &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.units</span></code></a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/version.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -96,11 +96,11 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <span class="target" id="module-MDAnalysis.version"></span><div class="section" id="version-information-for-mdanalysis-mdanalysis-version">
-<h1>10. Version information for MDAnalysis — <a class="reference internal" href="#module-MDAnalysis.version" title="MDAnalysis.version"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.version</span></tt></a><a class="headerlink" href="#version-information-for-mdanalysis-mdanalysis-version" title="Permalink to this headline">¶</a></h1>
-<p>The version information in <a class="reference internal" href="#module-MDAnalysis.version" title="MDAnalysis.version"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.version</span></tt></a> indicates the
+<h1>10. Version information for MDAnalysis — <a class="reference internal" href="#module-MDAnalysis.version" title="MDAnalysis.version"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.version</span></code></a><a class="headerlink" href="#version-information-for-mdanalysis-mdanalysis-version" title="Permalink to this headline">¶</a></h1>
+<p>The version information in <a class="reference internal" href="#module-MDAnalysis.version" title="MDAnalysis.version"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.version</span></code></a> indicates the
 release of MDAnalysis. MDAnalysis uses <a class="reference external" href="http://semver.org/">semantic versioning</a> as
 described in the wiki page on <a class="reference external" href="http://wiki.mdanalysis.org/SemanticVersioning">versioning of MDAnalysis</a>.</p>
 <p>In brief:</p>
@@ -121,14 +121,14 @@ <h1>10. Version information for MDAnalysis — <a class="reference internal" hre
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">Development versions and pre-releases have a suffix after
-the release number, such as <tt class="docutils literal"><span class="pre">0.11.0-dev</span></tt>. If you have
-problems, try out a full release (e.g. <tt class="docutils literal"><span class="pre">0.11.0</span></tt>) first.</p>
+the release number, such as <code class="docutils literal"><span class="pre">0.11.0-dev</span></code>. If you have
+problems, try out a full release (e.g. <code class="docutils literal"><span class="pre">0.11.0</span></code>) first.</p>
 </div>
 <div class="section" id="data">
 <h2>10.1. Data<a class="headerlink" href="#data" title="Permalink to this headline">¶</a></h2>
 <dl class="data">
 <dt id="MDAnalysis.version.__version__">
-<tt class="descclassname">MDAnalysis.version.</tt><tt class="descname">__version__</tt><em class="property"> = '0.11.0-dev'</em><a class="headerlink" href="#MDAnalysis.version.__version__" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.version.</code><code class="descname">__version__</code><em class="property"> = '0.11.0'</em><a class="headerlink" href="#MDAnalysis.version.__version__" title="Permalink to this definition">¶</a></dt>
 <dd><p>Release of MDAnalysis as a string, using <a class="reference external" href="http://semver.org/">semantic versioning</a>.</p>
 </dd></dl>
 
@@ -141,7 +141,7 @@ <h2>10.1. Data<a class="headerlink" href="#data" title="Permalink to this headli
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -156,10 +156,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="lib/util.html" title="9.9. Helper functions — MDAnalysis.lib.util"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -169,7 +169,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/visualization/streamlines.html b/package/doc/html/documentation_pages/visualization/streamlines.html
index 0ad496a6cdd..94ac3dd2745 100644
--- a/package/doc/html/documentation_pages/visualization/streamlines.html
+++ b/package/doc/html/documentation_pages/visualization/streamlines.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>8.1.1. 2D Streamplot &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>8.1.1. 2D Streamplot &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="8. Visualization modules" href="../visualization_modules.html" />
     <link rel="next" title="8.1.2. 3D Streamplot" href="streamlines_3D.html" />
     <link rel="prev" title="8. Visualization modules" href="../visualization_modules.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../visualization_modules.html" title="8. Visualization modules"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../visualization_modules.html" accesskey="U">8. Visualization modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../visualization_modules.html" accesskey="U">8. Visualization modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -66,12 +64,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="streamlines_3D.html"
                         title="next chapter">8.1.2. 3D Streamplot</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/visualization/streamlines.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/visualization/streamlines.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,13 +90,13 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="d-streamplot">
 <h1>8.1.1. 2D Streamplot<a class="headerlink" href="#d-streamplot" title="Permalink to this headline">¶</a></h1>
 <blockquote>
 <div><span class="target" id="module-MDAnalysis.visualization.streamlines"></span><div class="section" id="multicore-2d-streamplot-python-library-for-mdanalysis-mdanalysis-visualization-streamlines">
-<h2>8.1.1. Multicore 2D streamplot Python library for MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.visualization.streamlines" title="MDAnalysis.visualization.streamlines"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.visualization.streamlines</span></tt></a><a class="headerlink" href="#multicore-2d-streamplot-python-library-for-mdanalysis-mdanalysis-visualization-streamlines" title="Permalink to this headline">¶</a></h2>
+<h2>8.1.1. Multicore 2D streamplot Python library for MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.visualization.streamlines" title="MDAnalysis.visualization.streamlines"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.visualization.streamlines</span></code></a><a class="headerlink" href="#multicore-2d-streamplot-python-library-for-mdanalysis-mdanalysis-visualization-streamlines" title="Permalink to this headline">¶</a></h2>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -107,25 +107,25 @@ <h2>8.1.1. Multicore 2D streamplot Python library for MDAnalysis &#8212; <a clas
 </tr>
 <tr class="field-odd field"><th class="field-name">Copyright:</th><td class="field-body">GNU Public License v3</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Citation:</th><td class="field-body"><a class="reference internal" href="#chavent2014">[Chavent2014]</a></td>
+<tr class="field-even field"><th class="field-name">Citation:</th><td class="field-body"><a class="reference internal" href="#chavent2014" id="id1">[Chavent2014]</a></td>
 </tr>
 </tbody>
 </table>
 <dl class="function">
 <dt id="MDAnalysis.visualization.streamlines.generate_streamlines">
-<tt class="descclassname">MDAnalysis.visualization.streamlines.</tt><tt class="descname">generate_streamlines</tt><big>(</big><em>coordinate_file_path</em>, <em>trajectory_file_path</em>, <em>grid_spacing</em>, <em>MDA_selection</em>, <em>start_frame</em>, <em>end_frame</em>, <em>xmin</em>, <em>xmax</em>, <em>ymin</em>, <em>ymax</em>, <em>maximum_delta_magnitude</em>, <em>num_cores='maximum'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/visualization/streamlines.html#generate_streamlines"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.visualization.streamlines.generate_streamlines" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.visualization.streamlines.</code><code class="descname">generate_streamlines</code><span class="sig-paren">(</span><em>coordinate_file_path</em>, <em>trajectory_file_path</em>, <em>grid_spacing</em>, <em>MDA_selection</em>, <em>start_frame</em>, <em>end_frame</em>, <em>xmin</em>, <em>xmax</em>, <em>ymin</em>, <em>ymax</em>, <em>maximum_delta_magnitude</em>, <em>num_cores='maximum'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/visualization/streamlines.html#generate_streamlines"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.visualization.streamlines.generate_streamlines" title="Permalink to this definition">¶</a></dt>
 <dd><p>Produce the x and y components of a 2D streamplot data set.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first docutils">
 <dt><strong>coordinate_file_path</strong> <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
 <dd><p class="first last">Absolute path to the coordinate file</p>
 </dd>
 <dt><strong>trajectory_file_path</strong> <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
 <dd><p class="first last">Absolute path to the trajectory file. It will normally be desirable to filter the trajectory with a tool
-such as GROMACS g_filter (see <a class="reference internal" href="#chavent2014">[Chavent2014]</a>)</p>
+such as GROMACS g_filter (see <a class="reference internal" href="#chavent2014" id="id2">[Chavent2014]</a>)</p>
 </dd>
 <dt><strong>grid_spacing</strong> <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
 <dd><p class="first last">The spacing between grid lines (angstroms)</p>
@@ -162,7 +162,7 @@ <h2>8.1.1. Multicore 2D streamplot Python library for MDAnalysis &#8212; <a clas
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first docutils">
 <dt><strong>dx_array</strong> <span class="classifier-delimiter">:</span> <span class="classifier">array of floats</span></dt>
 <dd><p class="first last">An array object containing the displacements in the x direction</p>
 </dd>
@@ -178,25 +178,26 @@ <h2>8.1.1. Multicore 2D streamplot Python library for MDAnalysis &#8212; <a clas
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Examples :</th><td class="field-body"></td>
+<tr class="field-odd field"><th class="field-name">Examples:</th><td class="field-body"></td>
 </tr>
 </tbody>
 </table>
-<div class="highlight-python"><pre>import matplotlib, matplotlib.pyplot, numpy
+<div class="highlight-python"><div class="highlight"><pre>import matplotlib, matplotlib.pyplot, numpy
 import MDAnalysis, MDAnalysis.visualization.streamlines
 u1, v1, average_displacement,standard_deviation_of_displacement =
-MDAnalysis.visualization.streamlines.generate_streamlines('testing.gro','testing_filtered.xtc',grid_spacing =
-20, MDA_selection = 'name PO4',start_frame=2,end_frame=3,xmin=-8.73000049591,xmax= 1225.96008301,
+MDAnalysis.visualization.streamlines.generate_streamlines(&#39;testing.gro&#39;,&#39;testing_filtered.xtc&#39;,grid_spacing =
+20, MDA_selection = &#39;name PO4&#39;,start_frame=2,end_frame=3,xmin=-8.73000049591,xmax= 1225.96008301,
 ymin= -12.5799999237, ymax=1224.34008789,maximum_delta_magnitude = 1.0,num_cores=16)
 x = numpy.linspace(0,1200,61)
 y = numpy.linspace(0,1200,61)
 speed = numpy.sqrt(u1*u1 + v1*v1)
 fig = matplotlib.pyplot.figure()
-ax = fig.add_subplot(111,aspect='equal')
-ax.set_xlabel('x ($\AA$)')
-ax.set_ylabel('y ($\AA$)')
+ax = fig.add_subplot(111,aspect=&#39;equal&#39;)
+ax.set_xlabel(&#39;x ($\AA$)&#39;)
+ax.set_ylabel(&#39;y ($\AA$)&#39;)
 ax.streamplot(x,y,u1,v1,density=(10,10),color=speed,linewidth=3*speed/speed.max())
-fig.savefig('testing_streamline.png',dpi=300)</pre>
+fig.savefig(&#39;testing_streamline.png&#39;,dpi=300)
+</pre></div>
 </div>
 <img alt="../../_images/testing_streamline.png" src="../../_images/testing_streamline.png" />
 <table class="docutils citation" frame="void" id="chavent2014" rules="none">
@@ -219,7 +220,7 @@ <h2>8.1.1. Multicore 2D streamplot Python library for MDAnalysis &#8212; <a clas
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -234,11 +235,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../visualization_modules.html" title="8. Visualization modules"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../visualization_modules.html" >8. Visualization modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../visualization_modules.html" >8. Visualization modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -248,7 +249,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/visualization/streamlines_3D.html b/package/doc/html/documentation_pages/visualization/streamlines_3D.html
index 8ff2ae8efa5..2a6ff41c8f0 100644
--- a/package/doc/html/documentation_pages/visualization/streamlines_3D.html
+++ b/package/doc/html/documentation_pages/visualization/streamlines_3D.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>8.1.2. 3D Streamplot &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>8.1.2. 3D Streamplot &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../../index.html" />
     <link rel="up" title="8. Visualization modules" href="../visualization_modules.html" />
     <link rel="next" title="9. MDAnalysis library" href="../lib_modules.html" />
     <link rel="prev" title="8.1.1. 2D Streamplot" href="streamlines.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -51,11 +49,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="streamlines.html" title="8.1.1. 2D Streamplot"
              accesskey="P">previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../visualization_modules.html" accesskey="U">8. Visualization modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../visualization_modules.html" accesskey="U">8. Visualization modules</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../../index.html">
               <img class="logo" src="../../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -66,12 +64,14 @@ <h4>Previous topic</h4>
   <h4>Next topic</h4>
   <p class="topless"><a href="../lib_modules.html"
                         title="next chapter">9. MDAnalysis library</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/documentation_pages/visualization/streamlines_3D.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation_pages/visualization/streamlines_3D.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" />
@@ -90,13 +90,13 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="d-streamplot">
 <h1>8.1.2. 3D Streamplot<a class="headerlink" href="#d-streamplot" title="Permalink to this headline">¶</a></h1>
 <blockquote>
 <div><span class="target" id="module-MDAnalysis.visualization.streamlines_3D"></span><div class="section" id="multicore-3d-streamplot-python-library-for-mdanalysis-mdanalysis-visualization-streamlines-3d">
-<h2>8.1.2. Multicore 3D streamplot Python library for MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.visualization.streamlines_3D" title="MDAnalysis.visualization.streamlines_3D"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.visualization.streamlines_3D</span></tt></a><a class="headerlink" href="#multicore-3d-streamplot-python-library-for-mdanalysis-mdanalysis-visualization-streamlines-3d" title="Permalink to this headline">¶</a></h2>
+<h2>8.1.2. Multicore 3D streamplot Python library for MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.visualization.streamlines_3D" title="MDAnalysis.visualization.streamlines_3D"><code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.visualization.streamlines_3D</span></code></a><a class="headerlink" href="#multicore-3d-streamplot-python-library-for-mdanalysis-mdanalysis-visualization-streamlines-3d" title="Permalink to this headline">¶</a></h2>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -107,25 +107,25 @@ <h2>8.1.2. Multicore 3D streamplot Python library for MDAnalysis &#8212; <a clas
 </tr>
 <tr class="field-odd field"><th class="field-name">Copyright:</th><td class="field-body">GNU Public License v3</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Citation:</th><td class="field-body"><a class="reference internal" href="streamlines.html#chavent2014">[Chavent2014]</a></td>
+<tr class="field-even field"><th class="field-name">Citation:</th><td class="field-body"><a class="reference internal" href="streamlines.html#chavent2014" id="id1">[Chavent2014]</a></td>
 </tr>
 </tbody>
 </table>
 <dl class="function">
 <dt id="MDAnalysis.visualization.streamlines_3D.generate_streamlines_3d">
-<tt class="descclassname">MDAnalysis.visualization.streamlines_3D.</tt><tt class="descname">generate_streamlines_3d</tt><big>(</big><em>coordinate_file_path</em>, <em>trajectory_file_path</em>, <em>grid_spacing</em>, <em>MDA_selection</em>, <em>start_frame</em>, <em>end_frame</em>, <em>xmin</em>, <em>xmax</em>, <em>ymin</em>, <em>ymax</em>, <em>zmin</em>, <em>zmax</em>, <em>maximum_delta_magnitude=2.0</em>, <em>num_cores='maximum'</em><big>)</big><a class="reference internal" href="../../_modules/MDAnalysis/visualization/streamlines_3D.html#generate_streamlines_3d"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.visualization.streamlines_3D.generate_streamlines_3d" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">MDAnalysis.visualization.streamlines_3D.</code><code class="descname">generate_streamlines_3d</code><span class="sig-paren">(</span><em>coordinate_file_path</em>, <em>trajectory_file_path</em>, <em>grid_spacing</em>, <em>MDA_selection</em>, <em>start_frame</em>, <em>end_frame</em>, <em>xmin</em>, <em>xmax</em>, <em>ymin</em>, <em>ymax</em>, <em>zmin</em>, <em>zmax</em>, <em>maximum_delta_magnitude=2.0</em>, <em>num_cores='maximum'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/visualization/streamlines_3D.html#generate_streamlines_3d"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MDAnalysis.visualization.streamlines_3D.generate_streamlines_3d" title="Permalink to this definition">¶</a></dt>
 <dd><p>Produce the x, y and z components of a 3D streamplot data set.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first docutils">
 <dt><strong>coordinate_file_path</strong> <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
 <dd><p class="first last">Absolute path to the coordinate file</p>
 </dd>
 <dt><strong>trajectory_file_path</strong> <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
 <dd><p class="first last">Absolute path to the trajectory file. It will normally be desirable to filter the trajectory with a tool
-such as GROMACS g_filter (see <a class="reference internal" href="streamlines.html#chavent2014">[Chavent2014]</a>)</p>
+such as GROMACS g_filter (see <a class="reference internal" href="streamlines.html#chavent2014" id="id2">[Chavent2014]</a>)</p>
 </dd>
 <dt><strong>grid_spacing</strong> <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
 <dd><p class="first last">The spacing between grid lines (angstroms)</p>
@@ -168,7 +168,7 @@ <h2>8.1.2. Multicore 3D streamplot Python library for MDAnalysis &#8212; <a clas
 </dl>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><dl class="first docutils">
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first docutils">
 <dt><strong>dx_array</strong> <span class="classifier-delimiter">:</span> <span class="classifier">array of floats</span></dt>
 <dd><p class="first last">An array object containing the displacements in the x direction</p>
 </dd>
@@ -181,7 +181,7 @@ <h2>8.1.2. Multicore 3D streamplot Python library for MDAnalysis &#8212; <a clas
 </dl>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Examples :</th><td class="field-body"></td>
+<tr class="field-odd field"><th class="field-name">Examples:</th><td class="field-body"></td>
 </tr>
 </tbody>
 </table>
@@ -232,7 +232,7 @@ <h2>8.1.2. Multicore 3D streamplot Python library for MDAnalysis &#8212; <a clas
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -247,11 +247,11 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="streamlines.html" title="8.1.1. 2D Streamplot"
              >previous</a> |</li>
-        <li><a href="../../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li>
-          <li><a href="../visualization_modules.html" >8. Visualization modules</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li>
+          <li class="nav-item nav-item-1"><a href="../visualization_modules.html" >8. Visualization modules</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -261,7 +261,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/visualization_modules.html b/package/doc/html/documentation_pages/visualization_modules.html
index b09c8bf60ff..beb6f2baa4c 100644
--- a/package/doc/html/documentation_pages/visualization_modules.html
+++ b/package/doc/html/documentation_pages/visualization_modules.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>8. Visualization modules &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>8. Visualization modules &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,7 +14,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../',
-        VERSION:     '0.11.0-dev',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,15 +25,15 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="../_static/opensearch.xml"/>
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="../index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="../index.html" />
     <link rel="next" title="8.1.1. 2D Streamplot" href="visualization/streamlines.html" />
     <link rel="prev" title="7.5. Compute observable timeseries from trajectories — MDAnalysis.core.Timeseries" href="core/Timeseries.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -50,10 +48,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="core/Timeseries.html" title="7.5. Compute observable timeseries from trajectories — MDAnalysis.core.Timeseries"
              accesskey="P">previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="../index.html">
               <img class="logo" src="../_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -61,25 +59,25 @@ <h3>Navigation</h3>
   <h3><a href="../index.html">Table Of Contents</a></h3>
   <ul>
 <li><a class="reference internal" href="#">8. Visualization modules</a><ul>
-<li><a class="reference internal" href="#visualization-of-lipid-flow">8.1. Visualization of Lipid Flow</a><ul>
-</ul>
-</li>
+<li><a class="reference internal" href="#visualization-of-lipid-flow">8.1. Visualization of Lipid Flow</a></li>
 </ul>
 </li>
 </ul>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="core/Timeseries.html"
-                        title="previous chapter">7.5. Compute observable timeseries from trajectories &#8212; <tt class="docutils literal docutils literal docutils literal"><span class="pre">MDAnalysis.core.Timeseries</span></tt></a></p>
+                        title="previous chapter">7.5. Compute observable timeseries from trajectories &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.core.Timeseries</span></code></a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="visualization/streamlines.html"
                         title="next chapter">8.1.1. 2D Streamplot</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/documentation_pages/visualization_modules.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/documentation_pages/visualization_modules.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" />
@@ -98,13 +96,16 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="visualization-modules">
 <h1>8. Visualization modules<a class="headerlink" href="#visualization-modules" title="Permalink to this headline">¶</a></h1>
-<p>The MDAnalysis.visualization namespace contains code to carry out analyses which return data that is specifically-tailored for visualization.</p>
-<p>Please see the individual module documentation for additional references and citation information.</p>
-<p>These modules are not imported by default; in order to use them one has to import them from <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.visualization</span></tt>, for instance:</p>
+<p>The MDAnalysis.visualization namespace contains code to carry out analyses
+which return data that is specifically-tailored for visualization.</p>
+<p>Please see the individual module documentation for additional references and
+citation information.</p>
+<p>These modules are not imported by default; in order to use them one has to
+import them from <code class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.visualization</span></code>, for instance:</p>
 <div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">MDAnalysis.visualization.streamlines</span>
 </pre></div>
 </div>
@@ -129,7 +130,7 @@ <h2>8.1. Visualization of Lipid Flow<a class="headerlink" href="#visualization-o
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -144,10 +145,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="core/Timeseries.html" title="7.5. Compute observable timeseries from trajectories — MDAnalysis.core.Timeseries"
              >previous</a> |</li>
-        <li><a href="../index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="../index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -157,7 +158,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/genindex.html b/package/doc/html/genindex.html
index 2371b3027f3..7a734ec8ffb 100644
--- a/package/doc/html/genindex.html
+++ b/package/doc/html/genindex.html
@@ -1,7 +1,4 @@
 
-
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -10,15 +7,15 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>Index &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>Index &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '',
-        VERSION:     '0.11.0-dev',
+        URL_ROOT:    './',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -29,13 +26,13 @@
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="_static/opensearch.xml"/>
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="index.html" /> 
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="index.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -44,10 +41,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="index.html">
               <img class="logo" src="_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -55,7 +52,7 @@ <h3>Navigation</h3>
 
    
 
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="search.html" method="get">
       <input type="text" name="q" />
@@ -74,7 +71,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
 
 <h1 id="index">Index</h1>
@@ -263,23 +260,15 @@ <h2 id="A">A</h2>
   </dt>
 
       
-  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.align_principalAxis">align_principalAxis() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.align_principal_axis">align_principal_axis() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
       
-  <dt><a href="documentation_pages/analysis/align.html#MDAnalysis.analysis.align.alignto">alignto() (in module MDAnalysis.analysis.align)</a>
-  </dt>
-
-      
-  <dt><a href="documentation_pages/lib/KDTree/KDTree.html#MDAnalysis.lib.KDTree.KDTree.KDTree.all_get_indices">all_get_indices() (MDAnalysis.lib.KDTree.KDTree.KDTree method)</a>
-  </dt>
-
-      
-  <dt><a href="documentation_pages/lib/KDTree/KDTree.html#MDAnalysis.lib.KDTree.KDTree.KDTree.all_get_radii">all_get_radii() (MDAnalysis.lib.KDTree.KDTree.KDTree method)</a>
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.align_principalAxis">align_principalAxis() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
       
-  <dt><a href="documentation_pages/lib/KDTree/KDTree.html#MDAnalysis.lib.KDTree.KDTree.KDTree.all_search">all_search() (MDAnalysis.lib.KDTree.KDTree.KDTree method)</a>
+  <dt><a href="documentation_pages/analysis/align.html#MDAnalysis.analysis.align.alignto">alignto() (in module MDAnalysis.analysis.align)</a>
   </dt>
 
       
@@ -343,29 +332,29 @@ <h2 id="A">A</h2>
 
       </dl></dd>
       
-  <dt><a href="documentation_pages/lib/distances.html#MDAnalysis.lib.distances.applyPBC">applyPBC() (in module MDAnalysis.lib.distances)</a>, <a href="documentation_pages/lib/distances.html#MDAnalysis.lib.distances.applyPBC">[1]</a>
+  <dt><a href="documentation_pages/lib/distances.html#MDAnalysis.lib.distances.apply_PBC">apply_PBC() (in module MDAnalysis.lib.distances)</a>, <a href="documentation_pages/lib/distances.html#MDAnalysis.lib.distances.apply_PBC">[1]</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="documentation_pages/lib/transformations.html#MDAnalysis.lib.transformations.Arcball">Arcball (class in MDAnalysis.lib.transformations)</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="documentation_pages/lib/transformations.html#MDAnalysis.lib.transformations.arcball_nearest_axis">arcball_nearest_axis() (in module MDAnalysis.lib.transformations)</a>
   </dt>
 
       
-  <dt><a href="documentation_pages/lib/util.html#MDAnalysis.lib.util.asiterable">asiterable() (in module MDAnalysis.lib.util)</a>
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.as_Universe">as_Universe() (in module MDAnalysis.core.AtomGroup)</a>
   </dt>
 
       
-  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.asphericity">asphericity() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  <dt><a href="documentation_pages/lib/util.html#MDAnalysis.lib.util.asiterable">asiterable() (in module MDAnalysis.lib.util)</a>
   </dt>
 
       
-  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.asUniverse">asUniverse() (in module MDAnalysis.core.AtomGroup)</a>
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.asphericity">asphericity() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
       
@@ -413,7 +402,7 @@ <h2 id="A">A</h2>
   </dt>
 
       
-  <dt><a href="documentation_pages/lib/KDTree/NeighborSearch.html#MDAnalysis.lib.KDTree.NeighborSearch.AtomNeighborSearch">AtomNeighborSearch (class in MDAnalysis.lib.KDTree.NeighborSearch)</a>
+  <dt><a href="documentation_pages/lib/NeighborSearch.html#MDAnalysis.lib.NeighborSearch.AtomNeighborSearch">AtomNeighborSearch (class in MDAnalysis.lib.NeighborSearch)</a>
   </dt>
 
       
@@ -591,6 +580,14 @@ <h2 id="C">C</h2>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.center_of_geometry">center_of_geometry() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.center_of_mass">center_of_mass() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.CenterOfGeometry">CenterOfGeometry (class in MDAnalysis.core.Timeseries)</a>
   </dt>
 
@@ -870,6 +867,8 @@ <h2 id="C">C</h2>
   <dt><a href="documentation_pages/coordinates/DLPoly.html#MDAnalysis.coordinates.DLPoly.ConfigReader">ConfigReader (class in MDAnalysis.coordinates.DLPoly)</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="documentation_pages/units.html#MDAnalysis.units.constants">constants (in module MDAnalysis.units)</a>
   </dt>
@@ -878,8 +877,6 @@ <h2 id="C">C</h2>
   <dt><a href="documentation_pages/analysis/distances.html#MDAnalysis.analysis.distances.contact_matrix">contact_matrix() (in module MDAnalysis.analysis.distances)</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis">ContactAnalysis (class in MDAnalysis.analysis.contacts)</a>
   </dt>
@@ -1979,10 +1976,6 @@ <h2 id="C">C</h2>
   </dt>
 
       
-  <dt><a href="documentation_pages/lib/KDTree/NeighborSearch.html#MDAnalysis.lib.KDTree.NeighborSearch.CoordinateNeighborSearch">CoordinateNeighborSearch (class in MDAnalysis.lib.KDTree.NeighborSearch)</a>
-  </dt>
-
-      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates">coordinates() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -2398,10 +2391,6 @@ <h2 id="D">D</h2>
   </dt>
 
         
-  <dt><a href="documentation_pages/coordinates/TRZ.html#MDAnalysis.coordinates.TRZ.TRZReader.dt">(MDAnalysis.coordinates.TRZ.TRZReader attribute)</a>, <a href="documentation_pages/coordinates/TRZ.html#MDAnalysis.coordinates.TRZ.TRZReader.dt">[1]</a>
-  </dt>
-
-        
   <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.XTC.Timestep.dt">(MDAnalysis.coordinates.XTC.Timestep attribute)</a>
   </dt>
 
@@ -2425,10 +2414,6 @@ <h2 id="D">D</h2>
   <dt><a href="documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.dt">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute)</a>
   </dt>
 
-        
-  <dt><a href="documentation_pages/coordinates/xdrfile/core.html#MDAnalysis.coordinates.xdrfile.core.TrjReader.dt">(MDAnalysis.coordinates.xdrfile.core.TrjReader attribute)</a>
-  </dt>
-
       </dl></dd>
   </dl></td>
 </tr></table>
@@ -2743,23 +2728,23 @@ <h2 id="F">F</h2>
 
       <dd><dl>
         
-  <dt><a href="documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.Timestep.from_coordinates">(MDAnalysis.coordinates.DCD.Timestep class method)</a>
+  <dt><a href="documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.Timestep.from_coordinates">(MDAnalysis.coordinates.DCD.Timestep method)</a>
   </dt>
 
         
-  <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.TRR.Timestep.from_coordinates">(MDAnalysis.coordinates.TRR.Timestep class method)</a>
+  <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.TRR.Timestep.from_coordinates">(MDAnalysis.coordinates.TRR.Timestep method)</a>
   </dt>
 
         
-  <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.XTC.Timestep.from_coordinates">(MDAnalysis.coordinates.XTC.Timestep class method)</a>
+  <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.XTC.Timestep.from_coordinates">(MDAnalysis.coordinates.XTC.Timestep method)</a>
   </dt>
 
         
-  <dt><a href="documentation_pages/coordinates/xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep.from_coordinates">(MDAnalysis.coordinates.xdrfile.TRR.Timestep class method)</a>
+  <dt><a href="documentation_pages/coordinates/xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep.from_coordinates">(MDAnalysis.coordinates.xdrfile.TRR.Timestep method)</a>
   </dt>
 
         
-  <dt><a href="documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.Timestep.from_coordinates">(MDAnalysis.coordinates.xdrfile.XTC.Timestep class method)</a>
+  <dt><a href="documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.Timestep.from_coordinates">(MDAnalysis.coordinates.xdrfile.XTC.Timestep method)</a>
   </dt>
 
       </dl></dd>
@@ -2769,23 +2754,23 @@ <h2 id="F">F</h2>
 
       <dd><dl>
         
-  <dt><a href="documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.Timestep.from_timestep">(MDAnalysis.coordinates.DCD.Timestep class method)</a>
+  <dt><a href="documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.Timestep.from_timestep">(MDAnalysis.coordinates.DCD.Timestep method)</a>
   </dt>
 
         
-  <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.TRR.Timestep.from_timestep">(MDAnalysis.coordinates.TRR.Timestep class method)</a>
+  <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.TRR.Timestep.from_timestep">(MDAnalysis.coordinates.TRR.Timestep method)</a>
   </dt>
 
         
-  <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.XTC.Timestep.from_timestep">(MDAnalysis.coordinates.XTC.Timestep class method)</a>
+  <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.XTC.Timestep.from_timestep">(MDAnalysis.coordinates.XTC.Timestep method)</a>
   </dt>
 
         
-  <dt><a href="documentation_pages/coordinates/xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep.from_timestep">(MDAnalysis.coordinates.xdrfile.TRR.Timestep class method)</a>
+  <dt><a href="documentation_pages/coordinates/xdrfile/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep.from_timestep">(MDAnalysis.coordinates.xdrfile.TRR.Timestep method)</a>
   </dt>
 
         
-  <dt><a href="documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.Timestep.from_timestep">(MDAnalysis.coordinates.xdrfile.XTC.Timestep class method)</a>
+  <dt><a href="documentation_pages/coordinates/xdrfile/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.Timestep.from_timestep">(MDAnalysis.coordinates.xdrfile.XTC.Timestep method)</a>
   </dt>
 
       </dl></dd>
@@ -2874,10 +2859,6 @@ <h2 id="G">G</h2>
   </dt>
 
       
-  <dt><a href="documentation_pages/lib/KDTree/KDTree.html#MDAnalysis.lib.KDTree.KDTree.KDTree.get_indices">get_indices() (MDAnalysis.lib.KDTree.KDTree.KDTree method)</a>
-  </dt>
-
-      
   <dt><a href="documentation_pages/analysis/align.html#MDAnalysis.analysis.align.get_matching_atoms">get_matching_atoms() (in module MDAnalysis.analysis.align)</a>
   </dt>
 
@@ -2907,12 +2888,6 @@ <h2 id="G">G</h2>
   <dt><a href="documentation_pages/coordinates/PQR.html#MDAnalysis.coordinates.PQR.PQRReader.get_radii">get_radii() (MDAnalysis.coordinates.PQR.PQRReader method)</a>
   </dt>
 
-      <dd><dl>
-        
-  <dt><a href="documentation_pages/lib/KDTree/KDTree.html#MDAnalysis.lib.KDTree.KDTree.KDTree.get_radii">(MDAnalysis.lib.KDTree.KDTree.KDTree method)</a>
-  </dt>
-
-      </dl></dd>
       
   <dt><a href="documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.get_reader_for">get_reader_for() (in module MDAnalysis.coordinates.core)</a>
   </dt>
@@ -3014,15 +2989,9 @@ <h2 id="G">G</h2>
   </dt>
 
       
-  <dt><a href="documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.guess_format">guess_format() (in module MDAnalysis.coordinates.core)</a>
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.guess_format">(in module MDAnalysis.topology.core)</a>
+  <dt><a href="documentation_pages/lib/util.html#MDAnalysis.lib.util.guess_format">guess_format() (in module MDAnalysis.lib.util)</a>
   </dt>
 
-      </dl></dd>
       
   <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.guess_improper_dihedrals">guess_improper_dihedrals() (in module MDAnalysis.topology.core)</a>
   </dt>
@@ -3302,10 +3271,6 @@ <h2 id="K">K</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="documentation_pages/lib/KDTree/KDTree.html#MDAnalysis.lib.KDTree.KDTree.KDTree">KDTree (class in MDAnalysis.lib.KDTree.KDTree)</a>
-  </dt>
-
-      
   <dt><a href="documentation_pages/coordinates/TRZ.html#MDAnalysis.coordinates.TRZ.Timestep.kinetic_energy">kinetic_energy (MDAnalysis.coordinates.TRZ.Timestep attribute)</a>
   </dt>
 
@@ -3340,10 +3305,6 @@ <h2 id="L">L</h2>
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="documentation_pages/lib/KDTree/KDTree.html#MDAnalysis.lib.KDTree.KDTree.KDTree.list_search">list_search() (MDAnalysis.lib.KDTree.KDTree.KDTree method)</a>
-  </dt>
-
-      
   <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis.load">load() (MDAnalysis.analysis.contacts.ContactAnalysis method)</a>
   </dt>
 
@@ -3636,24 +3597,20 @@ <h2 id="M">M</h2>
   </dt>
 
       
-  <dt><a href="documentation_pages/lib/KDTree/KDTree.html#module-MDAnalysis.lib.KDTree.KDTree">MDAnalysis.lib.KDTree.KDTree (module)</a>
+  <dt><a href="documentation_pages/lib/log.html#module-MDAnalysis.lib.log">MDAnalysis.lib.log (module)</a>
   </dt>
 
       
-  <dt><a href="documentation_pages/lib/KDTree/NeighborSearch.html#module-MDAnalysis.lib.KDTree.NeighborSearch">MDAnalysis.lib.KDTree.NeighborSearch (module)</a>
+  <dt><a href="documentation_pages/lib/mdamath.html#module-MDAnalysis.lib.mdamath">MDAnalysis.lib.mdamath (module)</a>
   </dt>
 
       
-  <dt><a href="documentation_pages/lib/log.html#module-MDAnalysis.lib.log">MDAnalysis.lib.log (module)</a>
+  <dt><a href="documentation_pages/lib/NeighborSearch.html#module-MDAnalysis.lib.NeighborSearch">MDAnalysis.lib.NeighborSearch (module)</a>
   </dt>
 
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="documentation_pages/lib/mdamath.html#module-MDAnalysis.lib.mdamath">MDAnalysis.lib.mdamath (module)</a>
-  </dt>
-
-      
   <dt><a href="documentation_pages/lib/parallel.html#module-MDAnalysis.lib.parallel">MDAnalysis.lib.parallel (module)</a>
   </dt>
 
@@ -3900,6 +3857,10 @@ <h2 id="M">M</h2>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.moment_of_inertia">moment_of_inertia() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.momentOfInertia">momentOfInertia() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -4106,7 +4067,7 @@ <h2 id="N">N</h2>
   </dt>
 
       
-  <dt><a href="documentation_pages/exceptions.html#MDAnalysis.exceptions.NoDataError">NoDataError</a>, <a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.NoDataError">[1]</a>
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.NoDataError">NoDataError</a>, <a href="documentation_pages/exceptions.html#MDAnalysis.exceptions.NoDataError">[1]</a>
   </dt>
 
       
@@ -4274,6 +4235,10 @@ <h2 id="P">P</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.pack_into_box">pack_into_box() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.packIntoBox">packIntoBox() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -4538,6 +4503,10 @@ <h2 id="P">P</h2>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.principal_axes">principal_axes() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.principalAxes">principalAxes() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -4670,6 +4639,10 @@ <h2 id="R">R</h2>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.radius_of_gyration">radius_of_gyration() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.radiusOfGyration">radiusOfGyration() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -4791,12 +4764,12 @@ <h2 id="R">R</h2>
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.remove_anchor">remove_anchor() (MDAnalysis.core.AtomGroup.Universe method)</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="documentation_pages/topology/tpr_util.html#MDAnalysis.topology.tpr.obj.Params.reppow">reppow (MDAnalysis.topology.tpr.obj.Params attribute)</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.resample">resample() (MDAnalysis.analysis.density.Density method)</a>
   </dt>
@@ -4829,6 +4802,12 @@ <h2 id="R">R</h2>
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.resids">resids (MDAnalysis.core.AtomGroup.AtomGroup attribute)</a>
   </dt>
 
+      <dd><dl>
+        
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.resids">(MDAnalysis.core.AtomGroup.ResidueGroup attribute)</a>
+  </dt>
+
+      </dl></dd>
       
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Residue">Residue (class in MDAnalysis.core.AtomGroup)</a>
   </dt>
@@ -4859,6 +4838,10 @@ <h2 id="R">R</h2>
 
       <dd><dl>
         
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.resnames">(MDAnalysis.core.AtomGroup.ResidueGroup attribute)</a>
+  </dt>
+
+        
   <dt><a href="documentation_pages/topology/tpr_util.html#MDAnalysis.topology.tpr.obj.Atoms.resnames">(MDAnalysis.topology.tpr.obj.Atoms attribute)</a>
   </dt>
 
@@ -4871,6 +4854,12 @@ <h2 id="R">R</h2>
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.resnums">resnums (MDAnalysis.core.AtomGroup.AtomGroup attribute)</a>
   </dt>
 
+      <dd><dl>
+        
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.resnums">(MDAnalysis.core.AtomGroup.ResidueGroup attribute)</a>
+  </dt>
+
+      </dl></dd>
       
   <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ChainReader.rewind">rewind() (MDAnalysis.coordinates.base.ChainReader method)</a>
   </dt>
@@ -5114,39 +5103,9 @@ <h2 id="S">S</h2>
   </dt>
 
       
-  <dt><a href="documentation_pages/lib/KDTree/KDTree.html#MDAnalysis.lib.KDTree.KDTree.KDTree.search">search() (MDAnalysis.lib.KDTree.KDTree.KDTree method)</a>
+  <dt><a href="documentation_pages/lib/NeighborSearch.html#MDAnalysis.lib.NeighborSearch.AtomNeighborSearch.search">search() (MDAnalysis.lib.NeighborSearch.AtomNeighborSearch method)</a>
   </dt>
 
-      <dd><dl>
-        
-  <dt><a href="documentation_pages/lib/KDTree/NeighborSearch.html#MDAnalysis.lib.KDTree.NeighborSearch.AtomNeighborSearch.search">(MDAnalysis.lib.KDTree.NeighborSearch.AtomNeighborSearch method)</a>
-  </dt>
-
-        
-  <dt><a href="documentation_pages/lib/KDTree/NeighborSearch.html#MDAnalysis.lib.KDTree.NeighborSearch.CoordinateNeighborSearch.search">(MDAnalysis.lib.KDTree.NeighborSearch.CoordinateNeighborSearch method)</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="documentation_pages/lib/KDTree/NeighborSearch.html#MDAnalysis.lib.KDTree.NeighborSearch.AtomNeighborSearch.search_all">search_all() (MDAnalysis.lib.KDTree.NeighborSearch.AtomNeighborSearch method)</a>
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="documentation_pages/lib/KDTree/NeighborSearch.html#MDAnalysis.lib.KDTree.NeighborSearch.CoordinateNeighborSearch.search_all">(MDAnalysis.lib.KDTree.NeighborSearch.CoordinateNeighborSearch method)</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="documentation_pages/lib/KDTree/NeighborSearch.html#MDAnalysis.lib.KDTree.NeighborSearch.AtomNeighborSearch.search_list">search_list() (MDAnalysis.lib.KDTree.NeighborSearch.AtomNeighborSearch method)</a>
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="documentation_pages/lib/KDTree/NeighborSearch.html#MDAnalysis.lib.KDTree.NeighborSearch.CoordinateNeighborSearch.search_list">(MDAnalysis.lib.KDTree.NeighborSearch.CoordinateNeighborSearch method)</a>
-  </dt>
-
-      </dl></dd>
       
   <dt><a href="documentation_pages/lib/util.html#MDAnalysis.lib.util.NamedStream.seek">seek() (MDAnalysis.lib.util.NamedStream method)</a>
   </dt>
@@ -5163,6 +5122,16 @@ <h2 id="S">S</h2>
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.segids">segids (MDAnalysis.core.AtomGroup.AtomGroup attribute)</a>
   </dt>
 
+      <dd><dl>
+        
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.segids">(MDAnalysis.core.AtomGroup.ResidueGroup attribute)</a>
+  </dt>
+
+        
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.SegmentGroup.segids">(MDAnalysis.core.AtomGroup.SegmentGroup attribute)</a>
+  </dt>
+
+      </dl></dd>
       
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Segment">Segment (class in MDAnalysis.core.AtomGroup)</a>
   </dt>
@@ -5196,7 +5165,7 @@ <h2 id="S">S</h2>
 
       </dl></dd>
       
-  <dt><a href="documentation_pages/exceptions.html#MDAnalysis.exceptions.SelectionError">SelectionError</a>, <a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.SelectionError">[1]</a>
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.SelectionError">SelectionError</a>, <a href="documentation_pages/exceptions.html#MDAnalysis.exceptions.SelectionError">[1]</a>
   </dt>
 
       
@@ -5204,7 +5173,7 @@ <h2 id="S">S</h2>
   </dt>
 
       
-  <dt><a href="documentation_pages/exceptions.html#MDAnalysis.exceptions.SelectionWarning">SelectionWarning</a>, <a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.SelectionWarning">[1]</a>
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.SelectionWarning">SelectionWarning</a>, <a href="documentation_pages/exceptions.html#MDAnalysis.exceptions.SelectionWarning">[1]</a>
   </dt>
 
       
@@ -5274,15 +5243,23 @@ <h2 id="S">S</h2>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_altLocs">set_altLocs() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_bfactor">set_bfactor() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_bfactors">set_bfactors() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_charge">set_charge() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
       
-  <dt><a href="documentation_pages/lib/KDTree/KDTree.html#MDAnalysis.lib.KDTree.KDTree.KDTree.set_coords">set_coords() (MDAnalysis.lib.KDTree.KDTree.KDTree method)</a>
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_charges">set_charges() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
       
@@ -5293,17 +5270,29 @@ <h2 id="S">S</h2>
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_mass">set_mass() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_masses">set_masses() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
       
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_name">set_name() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_names">set_names() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_positions">set_positions() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_radii">set_radii() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_radius">set_radius() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -5318,6 +5307,16 @@ <h2 id="S">S</h2>
 
       </dl></dd>
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resids">set_resids() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      <dd><dl>
+        
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.set_resids">(MDAnalysis.core.AtomGroup.ResidueGroup method)</a>
+  </dt>
+
+      </dl></dd>
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resname">set_resname() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -5328,6 +5327,16 @@ <h2 id="S">S</h2>
 
       </dl></dd>
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resnames">set_resnames() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      <dd><dl>
+        
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.set_resnames">(MDAnalysis.core.AtomGroup.ResidueGroup method)</a>
+  </dt>
+
+      </dl></dd>
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resnum">set_resnum() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -5338,6 +5347,16 @@ <h2 id="S">S</h2>
 
       </dl></dd>
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resnums">set_resnums() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      <dd><dl>
+        
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup.set_resnums">(MDAnalysis.core.AtomGroup.ResidueGroup method)</a>
+  </dt>
+
+      </dl></dd>
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_segid">set_segid() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -5348,14 +5367,32 @@ <h2 id="S">S</h2>
 
       </dl></dd>
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_segids">set_segids() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      <dd><dl>
+        
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.SegmentGroup.set_segids">(MDAnalysis.core.AtomGroup.SegmentGroup method)</a>
+  </dt>
+
+      </dl></dd>
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_serial">set_serial() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_serials">set_serials() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_type">set_type() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_types">set_types() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_velocities">set_velocities() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -5372,6 +5409,10 @@ <h2 id="S">S</h2>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.shape_parameter">shape_parameter() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.shapeParameter">shapeParameter() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -5704,16 +5745,24 @@ <h2 id="T">T</h2>
   </dt>
 
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.total_charge">total_charge() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/coordinates/TRZ.html#MDAnalysis.coordinates.TRZ.Timestep.total_energy">total_energy (MDAnalysis.coordinates.TRZ.Timestep attribute)</a>
   </dt>
 
       
-  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.totalCharge">totalCharge() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.total_mass">total_mass() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
+  <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.totalCharge">totalCharge() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
+  </dt>
+
+      
   <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.totalMass">totalMass() (MDAnalysis.core.AtomGroup.AtomGroup method)</a>
   </dt>
 
@@ -6401,7 +6450,7 @@ <h2 id="X">X</h2>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -6410,10 +6459,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -6423,7 +6472,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/index.html b/package/doc/html/index.html
index 61b33c691b9..bbbe74e4692 100644
--- a/package/doc/html/index.html
+++ b/package/doc/html/index.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,15 +6,15 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>MDAnalysis documentation &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>MDAnalysis documentation &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '',
-        VERSION:     '0.11.0-dev',
+        URL_ROOT:    './',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,14 +25,14 @@
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="_static/opensearch.xml"/>
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="#" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="#" />
     <link rel="next" title="1. Overview over MDAnalysis" href="documentation_pages/overview.html" /> 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -46,10 +44,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="documentation_pages/overview.html" title="1. Overview over MDAnalysis"
              accesskey="N">next</a> |</li>
-        <li><a href="#">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="#">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="#">
               <img class="logo" src="_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -58,9 +56,7 @@ <h3><a href="#">Table Of Contents</a></h3>
   <ul>
 <li><a class="reference internal" href="#">MDAnalysis documentation</a><ul>
 <li><a class="reference internal" href="#citation">Citation</a></li>
-<li><a class="reference internal" href="#contents">Contents</a><ul>
-</ul>
-</li>
+<li><a class="reference internal" href="#contents">Contents</a></li>
 <li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -69,12 +65,14 @@ <h3><a href="#">Table Of Contents</a></h3>
   <h4>Next topic</h4>
   <p class="topless"><a href="documentation_pages/overview.html"
                         title="next chapter">1. Overview over MDAnalysis</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="_sources/index.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-<div id="searchbox" style="display: none">
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="_sources/index.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="search.html" method="get">
       <input type="text" name="q" />
@@ -93,7 +91,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <div class="section" id="mdanalysis-documentation">
 <h1>MDAnalysis documentation<a class="headerlink" href="#mdanalysis-documentation" title="Permalink to this headline">¶</a></h1>
@@ -101,9 +99,9 @@ <h1>MDAnalysis documentation<a class="headerlink" href="#mdanalysis-documentatio
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Release:</th><td class="field-body">0.11.0-dev</td>
+<tr class="field-odd field"><th class="field-name">Release:</th><td class="field-body">0.11.0</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Date:</th><td class="field-body">August 09, 2015</td>
+<tr class="field-even field"><th class="field-name">Date:</th><td class="field-body">September 07, 2015</td>
 </tr>
 </tbody>
 </table>
@@ -111,13 +109,13 @@ <h1>MDAnalysis documentation<a class="headerlink" href="#mdanalysis-documentatio
 toolkit to analyze molecular dynamics trajectories generated by
 <a class="reference external" href="http://www.charmm.org/">CHARMM</a>, <a class="reference external" href="http://www.gromacs.org/">Gromacs</a>, <a class="reference external" href="http://ambermd.org/">Amber</a>, <a class="reference external" href="http://www.ks.uiuc.edu/Research/namd/">NAMD</a>, <a class="reference external" href="http://lammps.sandia.gov/">LAMMPS</a>, or <a class="reference external" href="http://www.scd.stfc.ac.uk//44516.aspx">DL_POLY</a>; it also reads
 other formats (e.g. <a class="reference external" href="http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html">PDB</a> files and <a class="reference external" href="http://openbabel.org/wiki/XYZ_%28format%29">XYZ format</a> trajectories; see
-<a class="reference internal" href="documentation_pages/coordinates/init.html#id1"><em>Table of supported coordinate formats</em></a> for the full list). It can write
+<a class="reference internal" href="documentation_pages/coordinates/init.html#id1"><span>Table of supported coordinate formats</span></a> for the full list). It can write
 most of these formats, too, together with atom selections for use in
-<a class="reference external" href="http://www.gromacs.org/">Gromacs</a>, <a class="reference external" href="http://www.charmm.org/">CHARMM</a>, <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a> and <a class="reference external" href="http://www.pymol.org/">PyMol</a> (see <a class="reference internal" href="documentation_pages/selections_modules.html#selection-exporters"><em>Selection exporters</em></a>).</p>
+<a class="reference external" href="http://www.gromacs.org/">Gromacs</a>, <a class="reference external" href="http://www.charmm.org/">CHARMM</a>, <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a> and <a class="reference external" href="http://www.pymol.org/">PyMol</a> (see <a class="reference internal" href="documentation_pages/selections_modules.html#selection-exporters"><span>Selection exporters</span></a>).</p>
 <p>It allows one to read molecular dynamics trajectories and access the
 atomic coordinates through <a class="reference external" href="http://numpy.scipy.org">NumPy</a> arrays. This provides a flexible and
 relatively fast framework for complex analysis tasks. Fairly complete
-atom <a class="reference internal" href="documentation_pages/selections.html#selection-commands-label"><em>Selection Commands</em></a> are implemented. Trajectories can
+atom <a class="reference internal" href="documentation_pages/selections.html#selection-commands-label"><span>Selection Commands</span></a> are implemented. Trajectories can
 also be manipulated (for instance, fit to a reference structure) and
 written out in a range of formats.</p>
 <p><strong>Source code</strong> is available from
@@ -138,7 +136,7 @@ <h2>Citation<a class="headerlink" href="#citation" title="Permalink to this head
 <p>MDAnalysis also contains specific algorithms and whole analysis
 modules whose algorithms have also been published in the scientific
 literature. Please make sure to also reference any
-<a class="reference internal" href="documentation_pages/references.html#references-components"><em>Citations for included algorithms and modules</em></a> in published work.</p>
+<a class="reference internal" href="documentation_pages/references.html#references-components"><span>Citations for included algorithms and modules</span></a> in published work.</p>
 <p>Thank you!</p>
 </div>
 <div class="section" id="contents">
@@ -154,9 +152,9 @@ <h2>Contents<a class="headerlink" href="#contents" title="Permalink to this head
 <li class="toctree-l1"><a class="reference internal" href="documentation_pages/core_modules.html">7. Core modules</a></li>
 <li class="toctree-l1"><a class="reference internal" href="documentation_pages/visualization_modules.html">8. Visualization modules</a></li>
 <li class="toctree-l1"><a class="reference internal" href="documentation_pages/lib_modules.html">9. MDAnalysis library</a></li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_pages/version.html">10. Version information for MDAnalysis — <tt class="docutils literal"><span class="pre">MDAnalysis.version</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_pages/units.html">11. Constants and unit conversion &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.units</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_pages/exceptions.html">12. Custom exceptions and warnings &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.exceptions</span></tt></a></li>
+<li class="toctree-l1"><a class="reference internal" href="documentation_pages/version.html">10. Version information for MDAnalysis — <code class="docutils literal"><span class="pre">MDAnalysis.version</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="documentation_pages/units.html">11. Constants and unit conversion &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.units</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="documentation_pages/exceptions.html">12. Custom exceptions and warnings &#8212; <code class="docutils literal"><span class="pre">MDAnalysis.exceptions</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="documentation_pages/references.html">13. References</a></li>
 </ul>
 </div>
@@ -164,9 +162,9 @@ <h2>Contents<a class="headerlink" href="#contents" title="Permalink to this head
 <div class="section" id="indices-and-tables">
 <h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h2>
 <ul class="simple">
-<li><a class="reference internal" href="genindex.html"><em>Index</em></a></li>
-<li><a class="reference internal" href="py-modindex.html"><em>Module Index</em></a></li>
-<li><a class="reference internal" href="search.html"><em>Search Page</em></a></li>
+<li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
+<li><a class="reference internal" href="py-modindex.html"><span>Module Index</span></a></li>
+<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
 </ul>
 </div>
 </div>
@@ -177,7 +175,7 @@ <h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Pe
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -189,10 +187,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="documentation_pages/overview.html" title="1. Overview over MDAnalysis"
              >next</a> |</li>
-        <li><a href="#">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="#">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
     David Caplan, Matthieu Chavent, Xavier Deupi, Jan Domański, David L. Dotson
@@ -202,7 +200,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/objects.inv b/package/doc/html/objects.inv
index dab174964e4..164a2e5b535 100644
Binary files a/package/doc/html/objects.inv and b/package/doc/html/objects.inv differ
diff --git a/package/doc/html/py-modindex.html b/package/doc/html/py-modindex.html
index 8e20086f205..98bd315578e 100644
--- a/package/doc/html/py-modindex.html
+++ b/package/doc/html/py-modindex.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
@@ -8,15 +6,15 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>Python Module Index &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>Python Module Index &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '',
-        VERSION:     '0.11.0-dev',
+        URL_ROOT:    './',
+        VERSION:     '0.11.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -27,16 +25,16 @@
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="_static/opensearch.xml"/>
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="index.html" />
  
 
 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -45,15 +43,15 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="#" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="index.html">
               <img class="logo" src="_static/mdanalysis-logo-200x150.png" alt="Logo"/>
             </a></p>
-<div id="searchbox" style="display: none">
+<div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <form class="search" action="search.html" method="get">
       <input type="text" name="q" />
@@ -72,7 +70,7 @@ <h3>Quick search</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
 
    <h1>Python Module Index</h1>
@@ -89,472 +87,467 @@ <h1>Python Module Index</h1>
        <td><img src="_static/minus.png" class="toggler"
               id="toggle-1" style="display: none" alt="-" /></td>
        <td>
-       <tt class="xref">MDAnalysis</tt></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/align.html#module-MDAnalysis.analysis.align"><tt class="xref">MDAnalysis.analysis.align</tt></a></td><td>
+       <code class="xref">MDAnalysis</code></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/contacts.html#module-MDAnalysis.analysis.contacts"><tt class="xref">MDAnalysis.analysis.contacts</tt></a></td><td>
+       <a href="documentation_pages/analysis/align.html#module-MDAnalysis.analysis.align"><code class="xref">MDAnalysis.analysis.align</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/density.html#module-MDAnalysis.analysis.density"><tt class="xref">MDAnalysis.analysis.density</tt></a></td><td>
+       <a href="documentation_pages/analysis/contacts.html#module-MDAnalysis.analysis.contacts"><code class="xref">MDAnalysis.analysis.contacts</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/distances.html#module-MDAnalysis.analysis.distances"><tt class="xref">MDAnalysis.analysis.distances</tt></a></td><td>
+       <a href="documentation_pages/analysis/density.html#module-MDAnalysis.analysis.density"><code class="xref">MDAnalysis.analysis.density</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/gnm.html#module-MDAnalysis.analysis.gnm"><tt class="xref">MDAnalysis.analysis.gnm</tt></a></td><td>
+       <a href="documentation_pages/analysis/distances.html#module-MDAnalysis.analysis.distances"><code class="xref">MDAnalysis.analysis.distances</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/hbond_analysis.html#module-MDAnalysis.analysis.hbonds.hbond_analysis"><tt class="xref">MDAnalysis.analysis.hbonds.hbond_analysis</tt></a></td><td>
+       <a href="documentation_pages/analysis/gnm.html#module-MDAnalysis.analysis.gnm"><code class="xref">MDAnalysis.analysis.gnm</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/hbond_autocorrel.html#module-MDAnalysis.analysis.hbonds.hbond_autocorrel"><tt class="xref">MDAnalysis.analysis.hbonds.hbond_autocorrel</tt></a></td><td>
+       <a href="documentation_pages/analysis/hbond_analysis.html#module-MDAnalysis.analysis.hbonds.hbond_analysis"><code class="xref">MDAnalysis.analysis.hbonds.hbond_analysis</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/helanal.html#module-MDAnalysis.analysis.helanal"><tt class="xref">MDAnalysis.analysis.helanal</tt></a></td><td>
+       <a href="documentation_pages/analysis/hbond_autocorrel.html#module-MDAnalysis.analysis.hbonds.hbond_autocorrel"><code class="xref">MDAnalysis.analysis.hbonds.hbond_autocorrel</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/hole.html#module-MDAnalysis.analysis.hole"><tt class="xref">MDAnalysis.analysis.hole</tt></a></td><td>
+       <a href="documentation_pages/analysis/helanal.html#module-MDAnalysis.analysis.helanal"><code class="xref">MDAnalysis.analysis.helanal</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/leaflet.html#module-MDAnalysis.analysis.leaflet"><tt class="xref">MDAnalysis.analysis.leaflet</tt></a></td><td>
+       <a href="documentation_pages/analysis/hole.html#module-MDAnalysis.analysis.hole"><code class="xref">MDAnalysis.analysis.hole</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/nuclinfo.html#module-MDAnalysis.analysis.nuclinfo"><tt class="xref">MDAnalysis.analysis.nuclinfo</tt></a></td><td>
+       <a href="documentation_pages/analysis/leaflet.html#module-MDAnalysis.analysis.leaflet"><code class="xref">MDAnalysis.analysis.leaflet</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/psa.html#module-MDAnalysis.analysis.psa"><tt class="xref">MDAnalysis.analysis.psa</tt></a></td><td>
+       <a href="documentation_pages/analysis/nuclinfo.html#module-MDAnalysis.analysis.nuclinfo"><code class="xref">MDAnalysis.analysis.nuclinfo</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/rms.html#module-MDAnalysis.analysis.rms"><tt class="xref">MDAnalysis.analysis.rms</tt></a></td><td>
+       <a href="documentation_pages/analysis/psa.html#module-MDAnalysis.analysis.psa"><code class="xref">MDAnalysis.analysis.psa</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/waterdynamics.html#module-MDAnalysis.analysis.waterdynamics"><tt class="xref">MDAnalysis.analysis.waterdynamics</tt></a></td><td>
+       <a href="documentation_pages/analysis/rms.html#module-MDAnalysis.analysis.rms"><code class="xref">MDAnalysis.analysis.rms</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/analysis/x3dna.html#module-MDAnalysis.analysis.x3dna"><tt class="xref">MDAnalysis.analysis.x3dna</tt></a></td><td>
+       <a href="documentation_pages/analysis/waterdynamics.html#module-MDAnalysis.analysis.waterdynamics"><code class="xref">MDAnalysis.analysis.waterdynamics</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/init.html#module-MDAnalysis.coordinates.__init__"><tt class="xref">MDAnalysis.coordinates.__init__</tt></a></td><td>
+       <a href="documentation_pages/analysis/x3dna.html#module-MDAnalysis.analysis.x3dna"><code class="xref">MDAnalysis.analysis.x3dna</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/base.html#module-MDAnalysis.coordinates.base"><tt class="xref">MDAnalysis.coordinates.base</tt></a></td><td>
+       <a href="documentation_pages/coordinates/init.html#module-MDAnalysis.coordinates.__init__"><code class="xref">MDAnalysis.coordinates.__init__</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/core.html#module-MDAnalysis.coordinates.core"><tt class="xref">MDAnalysis.coordinates.core</tt></a></td><td>
+       <a href="documentation_pages/coordinates/base.html#module-MDAnalysis.coordinates.base"><code class="xref">MDAnalysis.coordinates.base</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/CRD.html#module-MDAnalysis.coordinates.CRD"><tt class="xref">MDAnalysis.coordinates.CRD</tt></a></td><td>
+       <a href="documentation_pages/coordinates/core.html#module-MDAnalysis.coordinates.core"><code class="xref">MDAnalysis.coordinates.core</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/DCD.html#module-MDAnalysis.coordinates.DCD"><tt class="xref">MDAnalysis.coordinates.DCD</tt></a></td><td>
+       <a href="documentation_pages/coordinates/CRD.html#module-MDAnalysis.coordinates.CRD"><code class="xref">MDAnalysis.coordinates.CRD</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/DLPoly.html#module-MDAnalysis.coordinates.DLPoly"><tt class="xref">MDAnalysis.coordinates.DLPoly</tt></a></td><td>
+       <a href="documentation_pages/coordinates/DCD.html#module-MDAnalysis.coordinates.DCD"><code class="xref">MDAnalysis.coordinates.DCD</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/DMS.html#module-MDAnalysis.coordinates.DMS"><tt class="xref">MDAnalysis.coordinates.DMS</tt></a></td><td>
+       <a href="documentation_pages/coordinates/DLPoly.html#module-MDAnalysis.coordinates.DLPoly"><code class="xref">MDAnalysis.coordinates.DLPoly</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/GMS.html#module-MDAnalysis.coordinates.GMS"><tt class="xref">MDAnalysis.coordinates.GMS</tt></a></td><td>
+       <a href="documentation_pages/coordinates/DMS.html#module-MDAnalysis.coordinates.DMS"><code class="xref">MDAnalysis.coordinates.DMS</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/GRO.html#module-MDAnalysis.coordinates.GRO"><tt class="xref">MDAnalysis.coordinates.GRO</tt></a></td><td>
+       <a href="documentation_pages/coordinates/GMS.html#module-MDAnalysis.coordinates.GMS"><code class="xref">MDAnalysis.coordinates.GMS</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/INPCRD.html#module-MDAnalysis.coordinates.INPCRD"><tt class="xref">MDAnalysis.coordinates.INPCRD</tt></a></td><td>
+       <a href="documentation_pages/coordinates/GRO.html#module-MDAnalysis.coordinates.GRO"><code class="xref">MDAnalysis.coordinates.GRO</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/LAMMPS.html#module-MDAnalysis.coordinates.LAMMPS"><tt class="xref">MDAnalysis.coordinates.LAMMPS</tt></a></td><td>
+       <a href="documentation_pages/coordinates/INPCRD.html#module-MDAnalysis.coordinates.INPCRD"><code class="xref">MDAnalysis.coordinates.INPCRD</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/MOL2.html#module-MDAnalysis.coordinates.MOL2"><tt class="xref">MDAnalysis.coordinates.MOL2</tt></a></td><td>
+       <a href="documentation_pages/coordinates/LAMMPS.html#module-MDAnalysis.coordinates.LAMMPS"><code class="xref">MDAnalysis.coordinates.LAMMPS</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/PDB.html#module-MDAnalysis.coordinates.PDB"><tt class="xref">MDAnalysis.coordinates.PDB</tt></a></td><td>
+       <a href="documentation_pages/coordinates/MOL2.html#module-MDAnalysis.coordinates.MOL2"><code class="xref">MDAnalysis.coordinates.MOL2</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/pdbextensions.html#module-MDAnalysis.coordinates.pdb.extensions"><tt class="xref">MDAnalysis.coordinates.pdb.extensions</tt></a></td><td>
+       <a href="documentation_pages/coordinates/PDB.html#module-MDAnalysis.coordinates.PDB"><code class="xref">MDAnalysis.coordinates.PDB</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/PDBQT.html#module-MDAnalysis.coordinates.PDBQT"><tt class="xref">MDAnalysis.coordinates.PDBQT</tt></a></td><td>
+       <a href="documentation_pages/coordinates/pdbextensions.html#module-MDAnalysis.coordinates.pdb.extensions"><code class="xref">MDAnalysis.coordinates.pdb.extensions</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/PQR.html#module-MDAnalysis.coordinates.PQR"><tt class="xref">MDAnalysis.coordinates.PQR</tt></a></td><td>
+       <a href="documentation_pages/coordinates/PDBQT.html#module-MDAnalysis.coordinates.PDBQT"><code class="xref">MDAnalysis.coordinates.PDBQT</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/TRJ.html#module-MDAnalysis.coordinates.TRJ"><tt class="xref">MDAnalysis.coordinates.TRJ</tt></a></td><td>
+       <a href="documentation_pages/coordinates/PQR.html#module-MDAnalysis.coordinates.PQR"><code class="xref">MDAnalysis.coordinates.PQR</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/TRR.html#module-MDAnalysis.coordinates.TRR"><tt class="xref">MDAnalysis.coordinates.TRR</tt></a></td><td>
+       <a href="documentation_pages/coordinates/TRJ.html#module-MDAnalysis.coordinates.TRJ"><code class="xref">MDAnalysis.coordinates.TRJ</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/TRZ.html#module-MDAnalysis.coordinates.TRZ"><tt class="xref">MDAnalysis.coordinates.TRZ</tt></a></td><td>
+       <a href="documentation_pages/coordinates/TRR.html#module-MDAnalysis.coordinates.TRR"><code class="xref">MDAnalysis.coordinates.TRR</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/xdrfile/core.html#module-MDAnalysis.coordinates.xdrfile.core"><tt class="xref">MDAnalysis.coordinates.xdrfile.core</tt></a></td><td>
+       <a href="documentation_pages/coordinates/TRZ.html#module-MDAnalysis.coordinates.TRZ"><code class="xref">MDAnalysis.coordinates.TRZ</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2"><tt class="xref">MDAnalysis.coordinates.xdrfile.libxdrfile2</tt></a></td><td>
+       <a href="documentation_pages/coordinates/xdrfile/core.html#module-MDAnalysis.coordinates.xdrfile.core"><code class="xref">MDAnalysis.coordinates.xdrfile.core</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/xdrfile/statno.html#module-MDAnalysis.coordinates.xdrfile.statno"><tt class="xref">MDAnalysis.coordinates.xdrfile.statno</tt></a></td><td>
+       <a href="documentation_pages/coordinates/xdrfile/libxdrfile2.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile2"><code class="xref">MDAnalysis.coordinates.xdrfile.libxdrfile2</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/xdrfile/TRR.html#module-MDAnalysis.coordinates.xdrfile.TRR"><tt class="xref">MDAnalysis.coordinates.xdrfile.TRR</tt></a></td><td>
+       <a href="documentation_pages/coordinates/xdrfile/statno.html#module-MDAnalysis.coordinates.xdrfile.statno"><code class="xref">MDAnalysis.coordinates.xdrfile.statno</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/xdrfile/XTC.html#module-MDAnalysis.coordinates.xdrfile.XTC"><tt class="xref">MDAnalysis.coordinates.xdrfile.XTC</tt></a></td><td>
+       <a href="documentation_pages/coordinates/xdrfile/TRR.html#module-MDAnalysis.coordinates.xdrfile.TRR"><code class="xref">MDAnalysis.coordinates.xdrfile.TRR</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/XTC.html#module-MDAnalysis.coordinates.XTC"><tt class="xref">MDAnalysis.coordinates.XTC</tt></a></td><td>
+       <a href="documentation_pages/coordinates/xdrfile/XTC.html#module-MDAnalysis.coordinates.xdrfile.XTC"><code class="xref">MDAnalysis.coordinates.xdrfile.XTC</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/coordinates/XYZ.html#module-MDAnalysis.coordinates.XYZ"><tt class="xref">MDAnalysis.coordinates.XYZ</tt></a></td><td>
+       <a href="documentation_pages/coordinates/XTC.html#module-MDAnalysis.coordinates.XTC"><code class="xref">MDAnalysis.coordinates.XTC</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/core/init.html#module-MDAnalysis.core.__init__"><tt class="xref">MDAnalysis.core.__init__</tt></a></td><td>
+       <a href="documentation_pages/coordinates/XYZ.html#module-MDAnalysis.coordinates.XYZ"><code class="xref">MDAnalysis.coordinates.XYZ</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/core/AtomGroup.html#module-MDAnalysis.core.AtomGroup"><tt class="xref">MDAnalysis.core.AtomGroup</tt></a></td><td>
+       <a href="documentation_pages/core/init.html#module-MDAnalysis.core.__init__"><code class="xref">MDAnalysis.core.__init__</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/core/Selection.html#module-MDAnalysis.core.Selection"><tt class="xref">MDAnalysis.core.Selection</tt></a></td><td>
+       <a href="documentation_pages/core/AtomGroup.html#module-MDAnalysis.core.AtomGroup"><code class="xref">MDAnalysis.core.AtomGroup</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/core/Timeseries.html#module-MDAnalysis.core.Timeseries"><tt class="xref">MDAnalysis.core.Timeseries</tt></a></td><td>
+       <a href="documentation_pages/core/Selection.html#module-MDAnalysis.core.Selection"><code class="xref">MDAnalysis.core.Selection</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/core/topologyobjects.html#module-MDAnalysis.core.topologyobjects"><tt class="xref">MDAnalysis.core.topologyobjects</tt></a></td><td>
+       <a href="documentation_pages/core/Timeseries.html#module-MDAnalysis.core.Timeseries"><code class="xref">MDAnalysis.core.Timeseries</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/exceptions.html#module-MDAnalysis.exceptions"><tt class="xref">MDAnalysis.exceptions</tt></a></td><td>
+       <a href="documentation_pages/core/topologyobjects.html#module-MDAnalysis.core.topologyobjects"><code class="xref">MDAnalysis.core.topologyobjects</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/lib/_distances.html#module-MDAnalysis.lib._distances"><tt class="xref">MDAnalysis.lib._distances</tt></a></td><td>
+       <a href="documentation_pages/exceptions.html#module-MDAnalysis.exceptions"><code class="xref">MDAnalysis.exceptions</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/lib/distances.html#module-MDAnalysis.lib.distances"><tt class="xref">MDAnalysis.lib.distances</tt></a></td><td>
+       <a href="documentation_pages/lib/_distances.html#module-MDAnalysis.lib._distances"><code class="xref">MDAnalysis.lib._distances</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/lib/KDTree/KDTree.html#module-MDAnalysis.lib.KDTree.KDTree"><tt class="xref">MDAnalysis.lib.KDTree.KDTree</tt></a></td><td>
+       <a href="documentation_pages/lib/distances.html#module-MDAnalysis.lib.distances"><code class="xref">MDAnalysis.lib.distances</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/lib/KDTree/NeighborSearch.html#module-MDAnalysis.lib.KDTree.NeighborSearch"><tt class="xref">MDAnalysis.lib.KDTree.NeighborSearch</tt></a></td><td>
+       <a href="documentation_pages/lib/log.html#module-MDAnalysis.lib.log"><code class="xref">MDAnalysis.lib.log</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/lib/log.html#module-MDAnalysis.lib.log"><tt class="xref">MDAnalysis.lib.log</tt></a></td><td>
+       <a href="documentation_pages/lib/mdamath.html#module-MDAnalysis.lib.mdamath"><code class="xref">MDAnalysis.lib.mdamath</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/lib/mdamath.html#module-MDAnalysis.lib.mdamath"><tt class="xref">MDAnalysis.lib.mdamath</tt></a></td><td>
+       <a href="documentation_pages/lib/NeighborSearch.html#module-MDAnalysis.lib.NeighborSearch"><code class="xref">MDAnalysis.lib.NeighborSearch</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/lib/parallel.html#module-MDAnalysis.lib.parallel"><tt class="xref">MDAnalysis.lib.parallel</tt></a></td><td>
+       <a href="documentation_pages/lib/parallel.html#module-MDAnalysis.lib.parallel"><code class="xref">MDAnalysis.lib.parallel</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/lib/parallel.html#module-MDAnalysis.lib.parallel.distances"><tt class="xref">MDAnalysis.lib.parallel.distances</tt></a></td><td>
+       <a href="documentation_pages/lib/parallel.html#module-MDAnalysis.lib.parallel.distances"><code class="xref">MDAnalysis.lib.parallel.distances</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/lib/qcprot.html#module-MDAnalysis.lib.qcprot"><tt class="xref">MDAnalysis.lib.qcprot</tt></a></td><td>
+       <a href="documentation_pages/lib/qcprot.html#module-MDAnalysis.lib.qcprot"><code class="xref">MDAnalysis.lib.qcprot</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/lib/transformations.html#module-MDAnalysis.lib.transformations"><tt class="xref">MDAnalysis.lib.transformations</tt></a></td><td>
+       <a href="documentation_pages/lib/transformations.html#module-MDAnalysis.lib.transformations"><code class="xref">MDAnalysis.lib.transformations</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/lib/util.html#module-MDAnalysis.lib.util"><tt class="xref">MDAnalysis.lib.util</tt></a></td><td>
+       <a href="documentation_pages/lib/util.html#module-MDAnalysis.lib.util"><code class="xref">MDAnalysis.lib.util</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/selections/base.html#module-MDAnalysis.selections.base"><tt class="xref">MDAnalysis.selections.base</tt></a></td><td>
+       <a href="documentation_pages/selections/base.html#module-MDAnalysis.selections.base"><code class="xref">MDAnalysis.selections.base</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/selections/charmm.html#module-MDAnalysis.selections.charmm"><tt class="xref">MDAnalysis.selections.charmm</tt></a></td><td>
+       <a href="documentation_pages/selections/charmm.html#module-MDAnalysis.selections.charmm"><code class="xref">MDAnalysis.selections.charmm</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/selections/gromacs.html#module-MDAnalysis.selections.gromacs"><tt class="xref">MDAnalysis.selections.gromacs</tt></a></td><td>
+       <a href="documentation_pages/selections/gromacs.html#module-MDAnalysis.selections.gromacs"><code class="xref">MDAnalysis.selections.gromacs</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/selections/jmol.html#module-MDAnalysis.selections.jmol"><tt class="xref">MDAnalysis.selections.jmol</tt></a></td><td>
+       <a href="documentation_pages/selections/jmol.html#module-MDAnalysis.selections.jmol"><code class="xref">MDAnalysis.selections.jmol</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/selections/pymol.html#module-MDAnalysis.selections.pymol"><tt class="xref">MDAnalysis.selections.pymol</tt></a></td><td>
+       <a href="documentation_pages/selections/pymol.html#module-MDAnalysis.selections.pymol"><code class="xref">MDAnalysis.selections.pymol</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/selections/vmd.html#module-MDAnalysis.selections.vmd"><tt class="xref">MDAnalysis.selections.vmd</tt></a></td><td>
+       <a href="documentation_pages/selections/vmd.html#module-MDAnalysis.selections.vmd"><code class="xref">MDAnalysis.selections.vmd</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/init.html#module-MDAnalysis.topology.__init__"><tt class="xref">MDAnalysis.topology.__init__</tt></a></td><td>
+       <a href="documentation_pages/topology/init.html#module-MDAnalysis.topology.__init__"><code class="xref">MDAnalysis.topology.__init__</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/base.html#module-MDAnalysis.topology.base"><tt class="xref">MDAnalysis.topology.base</tt></a></td><td>
+       <a href="documentation_pages/topology/base.html#module-MDAnalysis.topology.base"><code class="xref">MDAnalysis.topology.base</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/core.html#module-MDAnalysis.topology.core"><tt class="xref">MDAnalysis.topology.core</tt></a></td><td>
+       <a href="documentation_pages/topology/core.html#module-MDAnalysis.topology.core"><code class="xref">MDAnalysis.topology.core</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/CRDParser.html#module-MDAnalysis.topology.CRDParser"><tt class="xref">MDAnalysis.topology.CRDParser</tt></a></td><td>
+       <a href="documentation_pages/topology/CRDParser.html#module-MDAnalysis.topology.CRDParser"><code class="xref">MDAnalysis.topology.CRDParser</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/DLPolyParser.html#module-MDAnalysis.topology.DLPolyParser"><tt class="xref">MDAnalysis.topology.DLPolyParser</tt></a></td><td>
+       <a href="documentation_pages/topology/DLPolyParser.html#module-MDAnalysis.topology.DLPolyParser"><code class="xref">MDAnalysis.topology.DLPolyParser</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/DMSParser.html#module-MDAnalysis.topology.DMSParser"><tt class="xref">MDAnalysis.topology.DMSParser</tt></a></td><td>
+       <a href="documentation_pages/topology/DMSParser.html#module-MDAnalysis.topology.DMSParser"><code class="xref">MDAnalysis.topology.DMSParser</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/ExtendedPDBParser.html#module-MDAnalysis.topology.ExtendedPDBParser"><tt class="xref">MDAnalysis.topology.ExtendedPDBParser</tt></a></td><td>
+       <a href="documentation_pages/topology/ExtendedPDBParser.html#module-MDAnalysis.topology.ExtendedPDBParser"><code class="xref">MDAnalysis.topology.ExtendedPDBParser</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/GMSParser.html#module-MDAnalysis.topology.GMSParser"><tt class="xref">MDAnalysis.topology.GMSParser</tt></a></td><td>
+       <a href="documentation_pages/topology/GMSParser.html#module-MDAnalysis.topology.GMSParser"><code class="xref">MDAnalysis.topology.GMSParser</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/GROParser.html#module-MDAnalysis.topology.GROParser"><tt class="xref">MDAnalysis.topology.GROParser</tt></a></td><td>
+       <a href="documentation_pages/topology/GROParser.html#module-MDAnalysis.topology.GROParser"><code class="xref">MDAnalysis.topology.GROParser</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/HoomdXMLParser.html#module-MDAnalysis.topology.HoomdXMLParser"><tt class="xref">MDAnalysis.topology.HoomdXMLParser</tt></a></td><td>
+       <a href="documentation_pages/topology/HoomdXMLParser.html#module-MDAnalysis.topology.HoomdXMLParser"><code class="xref">MDAnalysis.topology.HoomdXMLParser</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/LAMMPSParser.html#module-MDAnalysis.topology.LAMMPSParser"><tt class="xref">MDAnalysis.topology.LAMMPSParser</tt></a></td><td>
+       <a href="documentation_pages/topology/LAMMPSParser.html#module-MDAnalysis.topology.LAMMPSParser"><code class="xref">MDAnalysis.topology.LAMMPSParser</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/MOL2Parser.html#module-MDAnalysis.topology.MOL2Parser"><tt class="xref">MDAnalysis.topology.MOL2Parser</tt></a></td><td>
+       <a href="documentation_pages/topology/MOL2Parser.html#module-MDAnalysis.topology.MOL2Parser"><code class="xref">MDAnalysis.topology.MOL2Parser</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/PDBParser.html#module-MDAnalysis.topology.PDBParser"><tt class="xref">MDAnalysis.topology.PDBParser</tt></a></td><td>
+       <a href="documentation_pages/topology/PDBParser.html#module-MDAnalysis.topology.PDBParser"><code class="xref">MDAnalysis.topology.PDBParser</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
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-       <a href="documentation_pages/topology/PDBQTParser.html#module-MDAnalysis.topology.PDBQTParser"><tt class="xref">MDAnalysis.topology.PDBQTParser</tt></a></td><td>
+       <a href="documentation_pages/topology/PDBQTParser.html#module-MDAnalysis.topology.PDBQTParser"><code class="xref">MDAnalysis.topology.PDBQTParser</code></a></td><td>
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+       <a href="documentation_pages/topology/PQRParser.html#module-MDAnalysis.topology.PQRParser"><code class="xref">MDAnalysis.topology.PQRParser</code></a></td><td>
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+       <a href="documentation_pages/topology/PrimitivePDBParser.html#module-MDAnalysis.topology.PrimitivePDBParser"><code class="xref">MDAnalysis.topology.PrimitivePDBParser</code></a></td><td>
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+       <a href="documentation_pages/topology/tables.html#module-MDAnalysis.topology.tables"><code class="xref">MDAnalysis.topology.tables</code></a></td><td>
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+       <a href="documentation_pages/topology/TOPParser.html#module-MDAnalysis.topology.TOPParser"><code class="xref">MDAnalysis.topology.TOPParser</code></a></td><td>
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+       <a href="documentation_pages/topology/tpr_util.html#module-MDAnalysis.topology.tpr"><code class="xref">MDAnalysis.topology.tpr</code></a></td><td>
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+       <a href="documentation_pages/topology/tpr_util.html#module-MDAnalysis.topology.tpr.obj"><code class="xref">MDAnalysis.topology.tpr.obj</code></a></td><td>
        <em></em></td></tr>
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-       <a href="documentation_pages/topology/tpr_util.html#module-MDAnalysis.topology.tpr.setting"><tt class="xref">MDAnalysis.topology.tpr.setting</tt></a></td><td>
+       <a href="documentation_pages/topology/tpr_util.html#module-MDAnalysis.topology.tpr.setting"><code class="xref">MDAnalysis.topology.tpr.setting</code></a></td><td>
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-       <a href="documentation_pages/topology/tpr_util.html#module-MDAnalysis.topology.tpr.utils"><tt class="xref">MDAnalysis.topology.tpr.utils</tt></a></td><td>
+       <a href="documentation_pages/topology/tpr_util.html#module-MDAnalysis.topology.tpr.utils"><code class="xref">MDAnalysis.topology.tpr.utils</code></a></td><td>
        <em></em></td></tr>
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-       <a href="documentation_pages/topology/TPRParser.html#module-MDAnalysis.topology.TPRParser"><tt class="xref">MDAnalysis.topology.TPRParser</tt></a></td><td>
+       <a href="documentation_pages/topology/TPRParser.html#module-MDAnalysis.topology.TPRParser"><code class="xref">MDAnalysis.topology.TPRParser</code></a></td><td>
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        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/topology/XYZParser.html#module-MDAnalysis.topology.XYZParser"><tt class="xref">MDAnalysis.topology.XYZParser</tt></a></td><td>
+       <a href="documentation_pages/topology/XYZParser.html#module-MDAnalysis.topology.XYZParser"><code class="xref">MDAnalysis.topology.XYZParser</code></a></td><td>
        <em></em></td></tr>
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        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/units.html#module-MDAnalysis.units"><tt class="xref">MDAnalysis.units</tt></a></td><td>
+       <a href="documentation_pages/units.html#module-MDAnalysis.units"><code class="xref">MDAnalysis.units</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/version.html#module-MDAnalysis.version"><tt class="xref">MDAnalysis.version</tt></a></td><td>
+       <a href="documentation_pages/version.html#module-MDAnalysis.version"><code class="xref">MDAnalysis.version</code></a></td><td>
        <em></em></td></tr>
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        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/visualization/streamlines.html#module-MDAnalysis.visualization.streamlines"><tt class="xref">MDAnalysis.visualization.streamlines</tt></a></td><td>
+       <a href="documentation_pages/visualization/streamlines.html#module-MDAnalysis.visualization.streamlines"><code class="xref">MDAnalysis.visualization.streamlines</code></a></td><td>
        <em></em></td></tr>
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        <td></td>
        <td>&nbsp;&nbsp;&nbsp;
-       <a href="documentation_pages/visualization/streamlines_3D.html#module-MDAnalysis.visualization.streamlines_3D"><tt class="xref">MDAnalysis.visualization.streamlines_3D</tt></a></td><td>
+       <a href="documentation_pages/visualization/streamlines_3D.html#module-MDAnalysis.visualization.streamlines_3D"><code class="xref">MDAnalysis.visualization.streamlines_3D</code></a></td><td>
        <em></em></td></tr>
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@@ -564,7 +557,7 @@ <h1>Python Module Index</h1>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -573,10 +566,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="#" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
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@@ -586,7 +579,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
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-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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 </html>
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diff --git a/package/doc/html/search.html b/package/doc/html/search.html
index f9047386348..759302bd264 100644
--- a/package/doc/html/search.html
+++ b/package/doc/html/search.html
@@ -1,5 +1,3 @@
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@@ -8,15 +6,15 @@
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-    <title>Search &mdash; MDAnalysis 0.11.0-dev documentation</title>
+    <title>Search &mdash; MDAnalysis 0.11.0 documentation</title>
     
     <link rel="stylesheet" href="_static/sphinxdoc.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '',
-        VERSION:     '0.11.0-dev',
+        URL_ROOT:    './',
+        VERSION:     '0.11.0',
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         FILE_SUFFIX: '.html',
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@@ -28,18 +26,20 @@
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     <script type="text/javascript" src="_static/searchtools.js"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within MDAnalysis 0.11.0-dev documentation"
+          title="Search within MDAnalysis 0.11.0 documentation"
           href="_static/opensearch.xml"/>
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
-    <link rel="top" title="MDAnalysis 0.11.0-dev documentation" href="index.html" />
+    <link rel="top" title="MDAnalysis 0.11.0 documentation" href="index.html" />
   <script type="text/javascript">
     jQuery(function() { Search.loadIndex("searchindex.js"); });
   </script>
+  
+  <script type="text/javascript" id="searchindexloader"></script>
    
 
   </head>
-  <body>
-    <div class="related">
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -48,10 +48,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-      <div class="sphinxsidebar">
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="index.html">
               <img class="logo" src="_static/mdanalysis-logo-200x150.png" alt="Logo"/>
@@ -62,7 +62,7 @@ <h3>Navigation</h3>
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          <div class="body">
+          <div class="body" role="main">
             
   <h1 id="search-documentation">Search</h1>
   <div id="fallback" class="admonition warning">
@@ -93,7 +93,7 @@ <h1 id="search-documentation">Search</h1>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related">
+    <div class="related" role="navigation" aria-label="related navigation">
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       <ul>
         <li class="right" style="margin-right: 10px">
@@ -102,10 +102,10 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li><a href="index.html">MDAnalysis 0.11.0-dev documentation</a> &raquo;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">MDAnalysis 0.11.0 documentation</a> &raquo;</li> 
       </ul>
     </div>
-    <div class="footer">
+    <div class="footer" role="contentinfo">
         &copy; Copyright 2005-2015, Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua Adelman,
     Christian Beckstein (logo), Alejandro Bernardin, Sébastien Buchoux,
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@@ -115,7 +115,7 @@ <h3>Navigation</h3>
     Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac Virshup,
     Zhuyi Xue, Carlos Yáñez S.,
     and Oliver Beckstein.
-      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
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   </body>
 </html>
\ No newline at end of file
diff --git a/package/doc/html/searchindex.js b/package/doc/html/searchindex.js
index defcbb0731c..0ffee329aa8 100644
--- a/package/doc/html/searchindex.js
+++ b/package/doc/html/searchindex.js
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Topology modules","3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <tt class=\"docutils literal docutils literal\"><span class=\"pre\">MDAnalysis.analysis.hole</span></tt>","9.3. KDTree module","7.5. Compute observable timeseries from trajectories &#8212; <tt class=\"docutils literal\"><span class=\"pre\">MDAnalysis.core.Timeseries</span></tt>","5.21.5. Status codes and symbols &#8212; <tt class=\"docutils literal docutils literal docutils literal\"><span class=\"pre\">statno</span></tt>","5.7. GRO file format &#8212; <tt class=\"docutils literal docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.GRO</span></tt>","9.3.2. Fast atom neighbor lookup using a KD tree (implemented in C++) &#8212; <tt class=\"docutils literal docutils literal\"><span class=\"pre\">MDAnalysis.lib.KDTree.NeighborSearch</span></tt>","11. Constants and unit conversion &#8212; <tt class=\"docutils literal docutils literal\"><span class=\"pre\">MDAnalysis.units</span></tt>","4.2. PSF topology parser","10. Version information for MDAnalysis \u2014 <tt class=\"docutils literal\"><span class=\"pre\">MDAnalysis.version</span></tt>","13. References","12. Custom exceptions and warnings &#8212; <tt class=\"docutils literal\"><span class=\"pre\">MDAnalysis.exceptions</span></tt>","5.1. Trajectory Readers and Writers  &#8212; <tt class=\"docutils literal docutils literal\"><span class=\"pre\">MDAnalysis.coordinates</span></tt>","4.13. Gromacs portable run input TPR format parser","4.4. CRD topology parser","7.2. Fundamental building blocks &#8212; <tt class=\"docutils literal\"><span class=\"pre\">MDAnalysis.core.AtomGroup</span></tt>","5.17. XYZ trajectory reader &#8212; <tt class=\"docutils literal docutils literal docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.XYZ</span></tt>","4.10. PQR topology parser","4.12. DESRES Molecular Structure file format topology parser","4.1. Topology readers &#8212; <tt class=\"docutils literal\"><span class=\"pre\">MDAnalysis.topology</span></tt>","3.5.2. HELANAL &#8212; analysis of protein helices","5.22. Extensions to <tt class=\"docutils literal\"><span class=\"pre\">Bio.PDB</span></tt> &#8212; <tt class=\"docutils literal\"><span class=\"pre\">pdb.extensions</span></tt>","4.3. AMBER PRMTOP topology parser","4.11. DL Poly format Topology Readers &#8212; <tt class=\"docutils literal\"><span class=\"pre\">MDAnalysis.topology.DLPolyParser</span></tt>","5.20. Common functions for coordinate reading &#8212; <tt class=\"docutils literal docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.core</span></tt>","4.8. Extended PDB topology parser","4.7. Primitive PDB topology parser","3.6.1. Generating densities from trajectories &#8212; <tt class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.density</span></tt>","4.14. MOL2 file format &#8212; <tt class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.MOL2</span></tt>","6.6. Base classes for the selection writers","8.1.2. 3D Streamplot","4.9. PDBQT topology parser","MDAnalysis documentation","6.2. PyMOL selections","5.16. Gromacs XTC file IO &#8212; <tt class=\"docutils literal docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.XTC</span></tt>","9.5. Mathematical helper functions &#8212; <tt class=\"docutils literal docutils literal\"><span class=\"pre\">MDAnalysis.lib.mdamath</span></tt>","9.2. Distance calculation library &#8212; <tt class=\"docutils literal docutils literal\"><span class=\"pre\">MDAnalysis.lib._distances</span></tt>","9.3.1. KDTree &#8212; <tt class=\"docutils literal\"><span class=\"pre\">MDAnalysis.KDTree.KDTree</span></tt>","8.1.1. 2D Streamplot","5.8. 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[4,5,44,59,61,90,96,97],tree:[0,36,45,47,63],treefilenam:0,tri:[8,17,25,35,44,59,85],triangl:11,triclin:[17,29,31,33,38,39,44,53,55],triclinic_box:55,triclinic_dimens:[17,29,31,33,38,39],triclinic_vector:[17,29,31,33,38,39,55],trigger:[29,31],tripl:[6,55,58],triplet:90,tripo:[24,35,79,90],trj:[0,11,23],trj_fit:11,trjconv:[29,31,38,39,40],trjname:44,trjname_fram:44,trjreader:[28,29,31,35,38,39,40],trjwriter:[29,31,38,39,40],trp:[5,45,63],trr:1,trrreader:[29,34,35,38],trrwriter:[29,34,35,38],truncat:[2,21,41,59],trzfilenam:30,trzreader:[30,35],trzwriter:[30,35],ts_class:78,ts_kwarg:78,tsjerk:55,tube:97,tube_filt:97,tune:9,tupl:[0,1,3,5,6,8,11,12,14,33,41,44,46,58,59,89,90,92],turn:[7,8],tweak:[20,32],twice:[6,47],twist:[7,14],twist_filenam:7,two:0,txt:[4,7],tyler:[96,97],type:[0,1,3],typeb:92,typeerror:[2,34,35,44],typic:[0,1,2,3,4,5,8,9,11,15,17,23,25,29,31,33,35,38,39,41,43,44,47,57,59,61,63,90,93],tyr:[5,45],u212b:94,u_dims_adk:61,u_eq_adk:61,u_fit:11,u_origin:11,u_refer:11,ucl:[4,7],unambigu:7,unchang:33,uncompress:59,under:[0,8,11,12,13,14,25,29,31,32,40,41,54,56,99],underflow:12,underli:[17,25,29,31,33,34,35,38,39,40,41,44,46,59,89],understand:[5,44],understood:[2,8,14,35,44,63],undesir:2,uniform:[7,28,58],uniqu:[11,44,94],unit:[2,7,8,13,17,23,25,28,29,30,31,32,33,35,38,39,40,41,44,47,50,53,55,58,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,91],unit_twist:7,unit_typ:94,unitcel:[17,21,23,25,26,29,31,32,33,35,38,39,40,41,44,53,55],uniti:2,unitless:77,univ:2,univers:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,17,21,23,24,25,27,29,31,32,33,35,38,39,40,43,44,46,47,54,55,57,58,59,61,63,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,92,93],unk:44,unknown:[2,44,74,80,81,84,89],unless:[0,1,17,23,25,29,31,33,35,38,39,44,58,59,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88],unlik:[23,29,31,35,40,41],unmodifi:[17,23,25,29,31,33,38,39,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88],unoffici:25,unpack:11,unpack_r:92,unpickl:44,unsign:41,unsolv:[29,31,38,39,40],unstabl:13,until:[5,25,35,41,44],unus:17,unvers:78,unzip:[1,61],updat:[5,9,10,12,25,29,35,38,41,47,54,58,61,89],update_select:5,update_selection1:5,update_selection2:5,upon:[29,31,38,39,40,44,88],upper:[2,9,35],ura:45,urey_bradlei:92,url:8,urllib2:59,urlopen:59,usabl:[29,64],use_kdtre:2,use_kdtree_routin:[47,63],use_model_flag:36,use_pbc:[44,47],use_periodic_select:[47,63],useful:[29,31,38,39,40],usefulli:8,user:[0,1,2,5,20,23,28,32,35,38,39,43,44,57,59,63,68,70,89,90,93],usual:[31,44,55,59],val:45,valid:[0,11,12,28,29,38,91],valu:[0,1,2,5,6,8,13,14,17,23,25,26,27,28,29,30,31,32,33,34,35,38,39,40,41,42,44,45],valueerror:[1,16,17,23,25,27,28,33,44,47,55,58,59,88,89,94],van:[8,58,89],vapor:13,vari:[71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88],variabl:[0,1],variant:83,variou:[9,35,47,60,89],vdw:[44,89],vdwradii:[44,89],vec1:55,vec2:55,vec3:55,vector:[10,13,17,29,31,33,35,38,39,40,41,44,46,53,55,56,58,61],vel:35,vel_arrai:[29,38],velavan:[7,62],veloc:[17,19,21,23,28,29,30,31,33,35,37,38,39,40,41,44,47,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88],velocity_sourc:[29,38],ver_str:92,verbos:[0,5,36],veri:[0,1,5,8,13,25,27,44,61,63,89],versa:5,versatil:14,version:[0,3,4,5,6,8,10,11,12,13,14,16,17,18,19,20,21,23,25,26,27,28,29,30,31,32,33,34,38,39,40,41,44,45,50,52,53,54,55,56,58,59,63,64,71,73,74,75,76,77,78,79,80,81,82,83,84,85],versionad:44,vertic:11,vesicl:[9,97],via:[6,29,38,44,59,61,63,94],vibrat:2,vice:5,view:[17,29,31,33,38,39,44],viol:92,vir:92,virtual:[7,58,92],visibl:44,visual:[2,8,14,64,70],viz:7,vmd:[2,5,8,9,17,32,44,45,64],vol:[8,13],volum:[2,13,17,29,31,33,35,38,39,55,94],volumetr:2,vsite2:92,vsite3:92,vsite3fad:92,vsite3fd:92,vsite3out:92,vsite4fd:92,vsite4fdn:92,vsiten:92,vtemp:92,waal:[8,89],wai:[0,1,2,4,5,8,9,13,35,44,47,58,59,61,63,64,65,66,67,68,69],wall:13,wallac:8,wang:8,want:[0,1,4,8,29,31,35,38,39,40,44,89],ward:11,warn:[2,5,25,36,44,47],wassenaar:55,wat:8,watch:17,water:[0,2,5,8],water_oxygen:44,water_shel:47,waterdipol:46,waterpol:92,watson:10,waveren:58,wc_pair:10,weak:[13,44],weakref:[29,30,31,38,39,40],webserv:7,weight:[0,11,12,57],weiner:8,welford1962:12,welford:12,well:[2,5,7,17,35,58,61],were:[3,5,17,25,29,33,38,41,44,47,63],weren:[17,31,33,39],what:[1,6,8,29,31,36,38,39,40,44,61],whatev:35,when:[0,1,2,3,5,7,8,11,12,14,17,23,25,27,29,31,32,33,34,35,38,39,40,41,44,47,50,53,55,58,59,62,63,64,65,66,67,68,69,89,90,94,95,99],whenc:[32,59],whenev:[2,35],where:[1,2,4,6,8,11,13,17,23,25,29,33,35,38,44,47,53,55,61,63,89,94],wherea:[0,44],wherev:86,whether:[6,14,17,28,29,30,31,33,35,38,39,41,44,47],which:[0,1,2,3,4,5,6,7,8,9,11,12,13,17,21,23,25,27,28,29,30,31,32,33,34,35,37,38,39,40,41,42,44,45,46,47,53,55,58,59,61,63,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,92,94,98],whilst:[6,35],white:[27,35,59,91],whitespac:[27,35,90,91],who:[35,90],whole:[0,1,2,5,8,12,14,17,25,28,29,31,32,33,35,38,39,40,41,44,47],whose:[5,7,8,99],why:59,wide:8,widget:97,width:[2,27,32,59],wiki:[36,55,90,95],wikipedia:55,wild:[0,8],wildcard:8,wildli:27,willi:2,willis1975:2,wilma:14,window:[7,13,58],wise:[1,3,11],wish:[6,8],within:[1,2,3,4,5,6,8,9,17,23,25,29,31,33,35,37,38,39,40,44,47,51,53,59,61,63,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89],without:[5,25,26,29,31,33,38,39,40,44],won:87,woolf:[61,62,99],wor:13,wor_analysi:13,wor_dip:13,wor_hh:13,wor_oh:13,work:[0,1,2,5,7,8,9,10,12,15,17,25,29,31,33,35,38,39,40],workaround:17,would:[0,5,17,23,25,35,54,63,94],wrap:[25,26,36,44,59],writabl:[41,59],write:[0,1,8,9,11,12,16,17,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,38,39,40,41,43,44,47,54,59,64,65,66,67,68,69,70,94,99],write_all_timestep:25,write_next_timestep:[17,23,25,28,29,31,32,35,38,39,40],write_pdb:36,write_preambl:[65,66,67,68,69],write_select:[9,44],write_simplerad2:8,write_trr:41,write_xtc:41,writelin:59,writepdb:78,writepsf:78,writer:[0,16,17,21,23],writt:2,written:[0,1,2,8,11,17,21,23,25,27,28,29,31,32,33,35,38,39,40,44,59,64,65,66,67,68,69,82,86,90,99],wrong:[17,23,25,36,46,56,58,63,89],wunsch:0,wwpdb:26,www:[8,26,45,58,99],x3dna_ensembl:14,x3dna_param:14,x3dnatraj:14,x84:94,x_axi:13,x_lower:97,x_upper:97,xab:94,xav:29,xavier:7,xaxi:58,xcen:44,xdna_ensembl:14,xdr:[29,31],xdrfile:[29,31,35],xdrfile_clos:41,xdrfile_open:41,xe2:94,xiang:14,xmax:[44,59,96,97],xmin:[44,59,96,97],xpbd:[35,90],xpdb:[35,74,84,90],xplor:[8,44,61,83,90],xpression:45,xrang:[3,53],xtc:[1,2,8,29],xtcreader:[31,34,35,39],xtcwriter:[31,34,35,39],xvg:7,xxx:[11,17,23,91],xxx_offset:0,xxxxxxxxyyyyyyyyzzzzzzzz:57,xyz:[13,21],xyz_v:21,xyzpars:[87,90],xyzplugin:32,xyzread:[32,34,35],xyzwrit:[32,35],xyzxyzxyzxyzxyzxyzxyzxyz:57,y_axi:13,y_lower:97,y_upper:97,yasp:[30,35],yaxi:58,ycen:44,year:[0,1,2,4,5,6,7,8,9,10,11,12,13,14,36,56,57,96,97],yeh1999:13,yeh:13,yerko:[13,62],yet:[21,36,50,58],yield:44,ylabel:8,ymax:[44,96,97],ymin:[44,96,97],you:[1,4,5,6,8,13,17,32,44,51,57,61,62,63,74,78,84,89,95,99],your:[5,8,14,17,44,47,92],yourself:[1,44,51],yshift:8,yuan:13,z_lower:97,z_plus_view:97,z_upper:97,z_valu:97,zaxi:58,zcen:44,zero:[11,32,41,59,77],zeta:[8,10],zhou:[13,62],zink:91,zip:[4,6,53,61],zlib:28,zmax:[13,44,63,97],zmin:[13,44,63,97],zone:[13,63],zvalu:[25,26]},titles:["3.1.1. Coordinate fitting and alignment &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.align</span></code>","3.1.2. Native contacts analysis &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.contacts</span></code>","3.6.1. Generating densities from trajectories &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.density</span></code>","3.1.3. Distance analysis &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.distances</span></code>","3.5.1. Elastic network analysis of MD trajectories &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.gnm</span></code>","3.2.1. Hydrogen Bond analysis &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.hbonds.hbond_analysis</span></code>","3.2.2. Hydrogen bond autocorrelation &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.hbonds.hbond_autocorrel</span></code>","3.5.2. HELANAL &#8212; analysis of protein helices","3.3.1. Generation and Analysis of HOLE pore profiles &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.hole</span></code>","3.3.2. Leaflet identification &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.leaflet</span></code>","3.4.1. Nucleic acid analysis &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.nuclinfo</span></code>","3.1.5. Calculating path similarity &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.psa</span></code>","3.1.4. Calculating root mean square quantities &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.rms</span></code>","3.6.2. Water dynamics analysis &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.waterdynamics</span></code>","3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.analysis.x3dna</span></code>","3. Analysis modules","5.2. CRD structure files in MDAnalysis &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.CRD</span></code>","5.3. DCD trajectory I/O  &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.DCD</span></code>","5.4. DL_Poly format reader <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.DLPoly</span></code>","5.5. DESRES file format &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.DMS</span></code>","5.6. GAMESS trajectory reader &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.GMS</span></code>","5.7. GRO file format &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.GRO</span></code>","5.8. INPCRD structure files in MDAnalysis &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.INPCRD</span></code>","5.9. LAMMPS DCD trajectory I/O  &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.LAMMPS</span></code>","5.10. MOL2 file format &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.MOL2</span></code>","5.11. PDB structure files in MDAnalysis &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.PDB</span></code>","5.12. PDBQT structure files in MDAnalysis &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.PDBQT</span></code>","5.13. PQR file format &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.PQR</span></code>","5.14. AMBER trajectories &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.TRJ</span></code>","5.15. Gromacs TRR file IO &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.TRR</span></code>","5.18. TRZ trajectory I/O  &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.TRZ</span></code>","5.16. Gromacs XTC file IO &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.XTC</span></code>","5.17. XYZ trajectory reader &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.XYZ</span></code>","5.19. Base classes &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.base</span></code>","5.20. Common functions for coordinate reading &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.core</span></code>","5.1. Trajectory Readers and Writers  &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates</span></code>","5.22. Extensions to <code class=\"docutils literal\"><span class=\"pre\">Bio.PDB</span></code> &#8212; <code class=\"docutils literal\"><span class=\"pre\">pdb.extensions</span></code>","5.21. NumPy access to Gromacs XDR trajectories &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.xdrfile</span></code>","5.21.2. Gromacs TRR trajectory I/O &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.xdrfile.TRR</span></code>","5.21.1. Gromacs XTC trajectory I/O &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.xdrfile.XTC</span></code>","5.21.3. Common high-level Gromacs XDR functionality &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.xdrfile.core</span></code>","5.21.4. The Gromacs XTC/TRR library <code class=\"docutils literal\"><span class=\"pre\">libxdrfile2</span></code>","5.21.5. Status codes and symbols &#8212; <code class=\"docutils literal\"><span class=\"pre\">statno</span></code>","5. Coordinates modules","7.2. Fundamental building blocks &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.core.AtomGroup</span></code>","7.3. Atom selection Hierarchy &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.core.Selection</span></code>","7.5. Compute observable timeseries from trajectories &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.core.Timeseries</span></code>","7.1. Core functions of MDAnalysis","7.4. Core Topology Objects &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.core.topologyobjects</span></code>","7. Core modules","12. Custom exceptions and warnings &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.exceptions</span></code>","9.3. Neighbor Search wrapper for MDAnalysis &#8212; :mod: <cite>MDAnalysis.lib.NeighborSearch</cite>","9.2. Distance calculation library &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.lib._distances</span></code>","9.1. Fast distance array computation &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.lib.distances</span></code>","9.4. Setting up logging &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.lib.log</span></code>","9.5. Mathematical helper functions &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.lib.mdamath</span></code>","9.6. Parallel algorithms for MDAnalysis","9.8. Fast QCP RMSD structure alignment &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.lib.qcprot</span></code>","9.7. Homogeneous Transformation Matrices and Quaternions &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.lib.transformations</span></code>","9.9. Helper functions &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.lib.util</span></code>","9. MDAnalysis library","1. Overview over MDAnalysis","13. References","2. Selection Commands","6.6. Base classes for the selection writers","6.4. CHARMM selections","6.3. Gromacs selections","6.5. Jmol selections","6.2. PyMOL selections","6.1. VMD selections","6. Selection exporters","4.4. CRD topology parser","4.11. DL Poly format Topology Readers &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.topology.DLPolyParser</span></code>","4.12. DESRES Molecular Structure file format topology parser","4.8. Extended PDB topology parser","4.17. GAMESS Topology Parser","4.5. GRO topology parser","4.18. HOOMD XML topology parser","4.16. LAMMPSParser","4.14. MOL2 file format &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.coordinates.MOL2</span></code>","4.6. PDB topology parser","4.9. PDBQT topology parser","4.10. PQR topology parser","4.2. PSF topology parser","4.7. Primitive PDB topology parser","4.3. AMBER PRMTOP topology parser","4.13. Gromacs portable run input TPR format parser","4.15. XYZ Topology Parser","4.19. Base topology reader classes &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.topology.base</span></code>","4.20. Common functions for topology building &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.topology.core</span></code>","4.1. Topology readers &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.topology</span></code>","4.21. MDAnalysis topology tables","4.22. Utility functions for the TPR topology parser","4. Topology modules","11. Constants and unit conversion &#8212; <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.units</span></code>","10. Version information for MDAnalysis \u2014 <code class=\"docutils literal\"><span class=\"pre\">MDAnalysis.version</span></code>","8.1.1. 2D Streamplot","8.1.2. 3D Streamplot","8. Visualization modules","MDAnalysis documentation"],titleterms:{"_distanc":52,"boolean":63,"class":[1,2,5,11,12,13,17,23,25,33,35,36,38,39,40,44,46,47,54,59,64,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,92],"default":[5,47],"export":70,"function":[0,2,4,7,11,12,34,36,40,41,44,47,53,54,55,57,58,59,89,92,94],access:37,acid:[10,15],algorithm:[56,62],align:[0,57],amber:[28,85],analysi:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15],angl:[10,90],angulardistribut:13,api:35,arrai:[53,56],ascii:28,atom:[5,44,45,63,90],atomgroup:44,attribut:35,autocorrel:6,background:7,base:[33,64,88,94],basic:46,binari:28,bio:36,biopython:25,block:44,bond:[5,6,15,90],bondord:90,build:[44,89],calcul:[11,12,52],charmm27:5,charmm:65,citat:[62,99],close:41,code:[42,61],combin:44,command:63,common:[0,34,40,89],comput:[46,53,56],connect:63,constant:[41,94],contact:[1,15],contain:59,content:99,conveni:54,convers:94,coordin:[0,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,37,38,39,40,43,79],core:[34,40,44,45,46,47,48,49,89],crd:[16,71],custom:50,data:[8,59,94,95],dcd:[17,23],decor:59,definit:92,densiti:2,deprec:78,descript:6,desr:[19,73],detect:5,develop:[86,90],dihedr:[10,90],dimension:1,directori:59,distanc:[3,10,15,52,53,56],dl_poli:18,dlpoli:18,dlpolypars:72,document:99,domain:12,dynam:13,elast:4,exampl:[1,5,6,8,12,13,14,24,25,41,58,61],except:50,extend:74,extens:[36,70],fast:[53,56,57],field:5,file:[16,19,21,22,24,25,26,27,29,31,32,41,59,70,73,79],fill:29,fit:0,flag:47,flow:98,footnot:94,forc:5,format:[18,19,21,24,27,32,35,72,73,79,86,90],frame:35,from:[2,41,46],fundament:44,gamess:[20,75],gener:[2,8,14,40,86],geometr:63,glycam06:5,gnm:4,gro:[21,76],gromac:[29,31,37,38,39,40,41,66,86],handl:59,hbond:[5,6],hbond_analysi:5,hbond_autocorrel:6,heavi:5,helan:7,helic:7,helicoid:14,helper:[0,11,55,59],hierarchi:[44,45],high:40,histori:35,hole:8,homogen:58,hoomd:77,hydrogen:[5,6,15],hydrogenbondlifetim:13,identif:9,implement:[25,94],improp:90,includ:[61,62],index:63,indic:99,inform:95,inpcrd:22,input:[6,86],instant:63,jmol:67,keyword:63,lammp:23,lammpspars:78,leaflet:9,level:40,lib:[51,52,53,54,55,56,57,58,59],librari:[41,52,60,62,96,97],libxdrfile2:41,lipid:98,list:[47,59],log:54,manipul:[44,59],mathemat:55,matric:58,mdamath:55,mdanalysi:[0,1,2,3,4,5,6,8,9,10,11,12,13,14,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,37,38,39,40,44,45,46,47,48,50,51,52,53,54,55,56,57,58,59,60,61,62,72,79,86,88,89,90,91,94,95,96,97,99],mean:12,meansquaredisplac:13,membran:15,merg:44,method:[11,35],mod:51,mode:29,modifi:63,modul:[15,29,31,43,49,62,93,98],mol2:[24,79],molecular:73,multicor:[96,97],multipl:12,name:[5,63,70],nativ:1,neighbor:51,neighborsearch:51,netcdf:28,network:4,note:[58,86,90,94],nucleic:[10,15],nuclinfo:10,numpi:37,object:[44,48],observ:46,open:41,order:[8,63],other:54,output:[5,6,13],over:61,overview:61,parallel:56,paramet:[8,14],pars:[59,86],parser:[71,73,74,75,76,77,80,81,82,83,84,85,86,87,92],path:11,pca:29,pdb:[25,36,74,80,84],pdbqt:[26,81],permiss:25,phase:10,poli:72,pore:8,portabl:86,pqr:[27,82],preexist:63,primit:84,privat:35,prmtop:85,profil:[8,14],protein:[7,15],psa:11,psf:83,purpos:54,pymol:68,python:[61,96,97],qcp:57,qcprot:57,quantiti:12,quaternion:58,read:[34,41,86],reader:[18,20,25,32,35,72,88,90],recogn:70,refer:[7,25,29,31,57,58,62,94],registri:35,replic:44,requir:58,resid:63,residu:[44,63],rmsd:[8,12,57],root:12,run:86,search:51,segment:[44,63],select:[45,63,64,65,66,67,68,69,70],selector:63,set:[54,92],similar:[11,63],simpl:[25,63],singl:[8,14,35],snippet:61,squar:12,statno:42,statu:[41,42],stream:59,streamlin:96,streamlines_3d:97,streamplot:[96,97],strict:25,string:59,structur:[8,14,15,16,22,25,26,57,73],support:[35,70,90,92],survivalprob:13,symbol:[41,42],system:44,tabl:[35,70,90,91,99],task:4,timeseri:46,timestep:35,tip:29,topolog:[44,48,71,72,73,74,75,76,77,80,81,82,83,84,85,86,87,88,89,90,91,92,93],topologyobject:48,tpr:[86,92],tprparser:[86,92],traj:28,trajectori:[2,4,8,14,17,20,23,28,30,32,35,37,38,39,46,61],transform:58,trick:29,trj:[28,40],trr:[29,38,41],trz:30,tutori:0,two:1,type:5,unit:94,usag:0,util:[4,8,14,59,92],valu:47,variabl:11,version:[86,95],visual:[96,97,98],vmd:69,volumetr:15,warn:50,water:13,waterdynam:13,waterorientationalrelax:13,whole:62,work:44,wrapper:51,writer:[25,35,64],x3dna:14,xdr:[37,40,41],xdrfile:[37,38,39,40],xml:77,xtc:[31,39,41],xyz:[32,87]}})
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